But fact is that you are interpreting it in the worst way, namely as if Bahamut is bound to do evil, instead of bound with limitations to what good he can do.
It's like the Dany bargaining with Tiamat debacle, his nature didn't allow him to resurrect us unless she declined Tiamat, but it was his choice, whether he would have resurrected us if Dany had declined Tiamat, there are rules and limitations upon what he can do, and there are certain things he has to do, but that don't mean that he has no free will, it just mean he has limited free will, there are still choices he makes himself, and we should try mainly to judge him by those, as opposed to judging him by what he's forbidden to do.
If it's indeed him in Slaver's Bay, then his nature probably forbid him taking more overt actions, but it don't require him to do what little he can, he could decide that it's not deserving of his help, but he choose not to do that.
In the same way there's a lot of things Yss can't do, and a lot of things he has to do, but those aren't what we judge our relationship with him on, we judge it on the merits, of those things he can decide whether to do or not.
In this case, Bahamut is probably limited, by strict rules of how much interference, a god without worshippers or sacrifices may do, he hasn't managed to find a suitable prophet to spread his words, so the extent of what he may do is low, he's however choosing to do what little he can, instead of declaring that until he has worshippers there it's not his problem.