No, I'm not suggesting that they are or ever were a secret couple, but rather that, at some point, something intimate happened between the two of them that Bella feels guilty about. Again, it doesn't have to be full sex, it could just be some kissing and groping but it still counts as intimacy shared between them and this is what Bella is referring to.
The fact that Jill has had guys come after her because of who she is could definitely be a factor in Bella's protectiveness of Jill, but it could also be compounded by feelings of guilt from Bella because of an intimate moment they shared as she feels like a hypocrite; trying to protect from Jill from men who want to take advantage of her but she feels like she did the same thing when Jill, most likely, had a moment of weakness. I could definitely see a scenario where, after getting upset because of a guy, Jill went to Bella for a shoulder to cry on and in the process of thanking Bella for always being there for her, Jill kissed her which led to a make-out and possible groping session.
One other thing is that one of the phone wallpapers you can get is of the two of them together. You can't even get a phone wallpaper of Josy and Maya but you can get one of Bella and Jill, which I can't help but feel is a little significant.