The Lincoln thing was the easy part, I think something like 7 out of 9 conspirators were Catholic. The Civil War? Think about the only country on the Americas that was not under some sort of control of the Roman Catholic church. Even Quebec, as Canada had not formed some independent status until 1869.
Well, I did do a little reading on the subject, and yes, several of the conspirators were Catholic, though the actual assassin was said to be less than strong in his beliefs, and may not have even been a Catholic. I couldn't find any actual ties to the Jesuits, just conjecture. There are several theories out there along with the Catholic one, so like Kennedy, it will probably remain fodder for the theorists.