I think he would be on her side as long as it aligned with whatever his agenda was at the time. And even if Emma wouldn’t allow him on her side, she might not have a choice.
Jefferson is after all the most nutral character we have seen yet.
If the purple cloud is bringing magic back to everyone then she would need a magic user on her side and i get the fealing that the fairy’s would be extreamly picky about when they would interfrear. They only seem to help extremely worthy people with one big wish or in cases like when the curse was comming. I think Emma would fight more dirty than the fairys would be willing to help with at least until it comes to a finalie worthy event.
I like the weird tension between them. I hope it stays that way
Between who? Jefferson and Regina or Jefferson and Emma? If my theory is right about Regina than their relation would have to shift (or at least the way we see it would). And the tension between Emma and Jefferson comes from the fact that it’s a last ditch effort of a desperate man. Depending on what happens with Grace getting her memories back and after he may be able to get rid of some of that desperateness.