The Short answer is no. First its worth nothing that Jefferson's opinion of the constitution evolved, while early on hoping for nine states to ratify and four states to hold out until a Bill of Rights was attached to by May 1788 Jefferson's opinion had changed to recommending ratification while recommending amendments. Jefferson was of course in France at the time, so his opinion was slow to make its way across the Atlantic but for whatever it is worth Madison speaking at the Virginia convention said that if Jefferson were in the convention he would vote for ratification. Interestingly the leader of the anti-federalists in Virginia, Patrick Henry, would later join the Federalist proto-party. To circle back though, while the Jeffersonian Republican proto-party likely did have more opponents of ratification in it than the Federalist party it would have been a minority faction within either party. The Federalist party did try to paint the Republicans as anti-federalists and Jefferson was aware that his party had many former anti-federalists within it and was careful not to promote that notion.

It should be noted that Federalist and Anti-Federalist don't always align in very clear camps. Especially early in the state ratification conventions some of the Federalists had advocated for ratification of the Constitution "as is" which alienated many who wanted to ratify with amendments. The federalists pretty quickly wised up however and stopped pressing this argument (especially apparent in New York ratification debates). The State federalists also had the advantage of moving quickly ratifying quickly in many of the smaller states, while the states where opposition to ratification was strongest, North Carolina, Virginia and New York had late conventions.