Northern leadership did not like Jews at all, southern leadership did
In those days, Jews were more prominent in the South than in the North. They were white and didn’t rock the boat so Southern elites got along well with them. Jews weren’t yet as prominent in the North so Northern elites didn’t think about them very much.
After the war, as Jews became wealthier, Northern elites came to see them as a threat and wanted to exclude them from their social clubs and resort hotels. Much later of course, Southern leaders came to see Jews from the North as a threat and didn’t like them either.
In any case, in 1860, Jews who came to the North from Germany largely supported the Union, as the other immigrants from Germany did.