I infiltrated a cult, but now I think I want to join them. Should I?
There's really no difference other than the alignment points, and possibly companion affection.
Either way, you'll gain the 'Revanite' title, the same XP and item rewards, and after a little while, a letter with some credits from whoever you sided with.
There's no lasting impact, though this isn't the last of Revan's legacy with which you'll interact.