I'm in the process of leveling another toon, and was curious when Acina wants to ally with you to defeat Valynn if you choose not to, does it really have any effect on the story aside from a minor conversation it would change during the Iokath part? I just allied with them well if I play an Empire toon its a no brainer, but for a Republic toon what actually happens if you don't ally? All that I really noticed was getting letters in the mail from Acina and Vowrawn here and there.

No, the only difference is minor dialogue (and email) changes during Kotet and War for Iokath. The decision on Iokath is the only deciding factor for that part of the storyline. Edited July 17, 2020 by OldVengeance

I'm guessing it probably made more sense at the time when Ihey were released at separate times. I think this commando I'll just not ally with her for a change.