In the 17th century, Presbyterians argued for their ecclesiology from the structure of the Jewish church. It was divided geographically and functioned with varying levels of authority (presbytery, general assembly, etc). Gillespie said “it is plain from Scripture that there was at least a two-fold ecclesiastical court among the Jews, the synagogue and the sanhedrim, the latter having authority above the former.” An important part of this argument was distinguishing between the church and the state in Israel. “That there was an high ecclesiastical sanhedrim, distinct from the civil sanhedrim, is observed by Pelargus, on Deut. 17., and Sopingius, ad Bonam Fidem Sibrandi, p. 261, et seq., beside many others cited before, part 1, chapter 11. And that it was so we prove from three places of the Old Testament… We find Deut. 17, a distinction of two supreme judicatories, to be set in the place which the Lord should choose to put his name there,—the one of the priests and Levites, the other of the judges.” Both the Episcopalians and the Separatists/Congregationalists argued that appeal cannot be made to Israel. In response, Gillespie argued
Is it right dealing now to forbid us to reason from the form of the Jews? I will not use any further expostulation, but let the reader judge. The truth is this: Even as that which is in a child, as he is a child, agreeth not to a man, yet that which is in a child, as he is animal rationale, agreeth also to a man; so what we find in the Jewish church, as it was Jewish, or in infancy, and under the pedagogy of the law, agreeth not indeed to the Christian church. But whatsoever the Jewish church had, as it was a political church, or ecclesiastical republic (of which sort of things the diversity and subordination of ecclesiastical courts was one), doth belong by the same reason to the Christian church. I say further, though the commonwealth and civil policy of the Jews be not in all points a pattern to our civil policy, yet I am sure it is no error to imitate the civil policy of the Jews in such things as they had, not for any special reason proper to them, but are common to all well constituted commonwealths; and so we may argue from their commonwealth, that it is a good policy to have divers civil courts, and the higher to receive appellations from the inferior, as it was among them. Shall we not, by the very like reason, fetch from their ecclesiastical republic diversity of spiritual courts, and the supreme to receive appellations from the inferior, because so was the constitution of the Jewish church, and that under the common respect and account of a political church, and not for any special reason which doth not concern us?
The Church of England should derive it’s ecclesiastical polity from the Jewish church, and the commonwealth of England should derive its civil polity from the commonwealth of Israel.
In an essay titled Goodwin vs. Gillespie: An Old Testament Debate for Church Polity, Jonathan Brack summarizes a debate that took place in the Westminster Assembly between the Presbyterians and the Congregationalists.
Mr. Calamy argues for a Gillespie-like understanding of a distinction between civil and ecclesiastical courts from Deuteronomy 17:12:
Here is a distinctive that hints 2 courts. By ‘priests’ is not meant one priest but many. By “Judge” cannot be meant the high priest, for he is contradistinct from the priest. 2. Cron. 19:8–11 ther is the resistution of them by Jehosaphat. This text showes the distinction of the Judicatories. The words in the 8 v. read with a reduplication.
Goodwin, a Congregationalist, objected.
In questioning the often-used Deut. 17: 8–9 and 2 Chron. 35:8 texts posed by Gillespie, where Gillespie demonstrated a distinction between church and state in the Old Testament, Goodwin showed himself to be functioning from a different hermeneutical angle. An angle that disagreed on the status and nature of the Jewish church in the Old Testament,
That which belonged to this Sanhedrin at Jerusalem, it was either matters Judiciall, therefore called ‘matters of the Lord’ because God had given expresse … Or matters of the king, the things of his revenew, or perhaps matters of warre and peace, yet soe as they did not … The church & state ware involved in one. Their lawes ware the lawes of God. Their judicialls had spirituals in them. 
Goodwin along with Phillip Nye challenged the distinction between civil and ecclesiastical.
Phillip Nye launched into a long speech attempting to disprove the civil and ecclesiastical distinction made from Deuteronomy 17:8–9.
The matter before us is about the validity of this place of scripture to prove that besides the priests an addition of elders. My concievements are that the totum totalum of the common wealth ware of a mixt nature … Ther is no such a perpetuall intermixture throughout all as in the Jewish church.
Goodwin’s point was that everything given in Deuteronomy was “ecclesiastical” in a certain sense. This was because, for Goodwin, ecclesiastical and civil are one and the same in the Old Testament. To this, Lord Say added that on these grounds,
It ware much better to find out those places that established a ground for this ruling elder in the New Testament wher this constitution was.
So the Congregationlists argued that Israel was a unique entity of a “mixt nature” that cannot be appealed to in order to establish church government under the New Covenant.
Brack goes on to highlight how the Presbyterians pointed out inconsistencies in the Congregationalists on this point.
After Calamy represents the basic Presbyterian position of Old Testament roots for elder-rule, Gillespie strengthens the argument by arguing for hermeneutical implications,
Something to strengthen what is spoken. The analogy betwixt Jewish & Christian church, little question of that little question… If this faile, the argument of Baptisme from circumcision will faile also.
…How can the Assembly agree to pedo-baptism by appealing to the Old Testament, without also functioning the same way for the debate on church polity?… If one were to cut loose the Old Testament ground for elder rule, then one were to cut loose the very ground for Presbyterianism, not to mention baptism…
To this Mr. Vines pressed Goodwin and Lord Say on the exact same hermeneutical point made by Gillespie two days earlier,
For that we must not looke to the state of the Jewish church, is only a warrantableness for the analogy of the Old Testament & New, granted. The brother that spake last said before we must cut loose the argument of Jewish church; [for] but how shall we prove pedo-Baptism?
Richard Vines saw the inconsistency in hermeneutical method being deployed by the Congregationalists. If we were to cut loose the Old Testament ground for church polity, then what is to stop us from the Anabaptist tenet of cutting loose our progeny as well?
In 1953, in an essay titled The Relevance of the Theocracy, Kline wrote a short essay arguing against appeal to Israel for matters of civil government and ecclesiology. He said any such appeal is unwarranted because Israel was a unique theocratic entity unlike any other. It was a type of heaven. As a result, “church” and “state” were of a “mixt nature.”
If we do listen we will not try to segment the Theocracy into the usual three discrete institutions. We will not then say: “Here (e.g. in Aaron) is the church, and here (e.g. in Moses or David) is the state, and there the family.” Not even roughly speaking. For all that can be said accurately is, “Here are theocratic priests, here are theocratic kings, here are theocratic prophets and there are the theocratic people from whose ranks all these have come. (Cf. Ex. 28:1; Dt. 17:5; 18:5.)…
That the horns of the dilemma are vaporous is evident, for the argument rests on an utterly false equation of the theocratic monarchy with the ordinary state. As observed above, neither church nor state is isolable within the Theocracy. It is therefore impossible to identify one theocratic institution such as the kingship with the ordinary concept of the state…
Our chief criticism again, in terms of the thesis of this article, is that to label the priests and/or the prophets as the church within the Theocracy [as the Presbyterians did] is unwarranted… God was in the midst of the covenant people and, therefore, all was church, as also all was family and all state – the church of God, the family of God, the Kingdom of God – all in one and one in all, and such was the Theocracy. However, if all is church and all is family and all is state, then nothing is church and nothing is family and nothing is state in the usual sense of those words. Strictly speaking all is Theocracy and nothing but Theocracy.
Like many modern Presbyterians, Kline has neglected the roots of Presbyterianism and is unaware that he has adopted the Congregationalist hermeneutic (see my post on Congregationalist covenant theology).
I will close with these words from Brack:
In recent church polity debates among Presbyterians and Particularists… appealing to Old Testament ecclesiastical polity in order to gain support for the purported theories of New Testament polity assumes a presupposed debated hermeneutical method. In other words, a foul is committed in the debate, since a disagreement over how one uses the Old Testament is not properly neutral. This truth, in the mind of many Presbyterians, is a strange inconsistency in the pattern of basic Reformed hermeneutic strategies.
Recognizing that Israel in the land of Canaan was a type of heaven necessarily leads to congregtaionalism and the rejection of paedobaptism, as Presbyterians warned from the beginning.