Honestly, it's hard to say. It is radical to offer office only to Christians and to allow only Christians as U.S. citizens, but the context of the times must be considered. The U.S. at that time was 99% Christian. There were hardly any other religions to speak of in America at that time (smattering of catholics and jewish citizens). It was a Christian nation - that's a simple historical fact. John Jay's motives may have been good - I can't read his motives, and I can't put myself in 1790.
In any case, no man is perfect and he may be wrong for refusing citizenship to catholics regardless of the consensus.
Regardless, he was a contributor to the Federalist papers and the first chief justice of the Supreme Court, and he was a true believer in my opinion. So God will be his judge. I can't see a man's motive - only God can. And I believe the answer lies in his motive.
I thought that one of the biggest things that conservatives criticized the left for was wanting to be judged based on intent rather than results.