What are the odds my former professor will say something, if I tell her I was afraid to bug her for a letter of recommendation?

Definitely do. And, if its not too late, ask her to still send one. In any case, if she gets upset, it will only be because you didn't ask. By the way, asking a former professor for a recommendation is standard. Every professor I've known, including myself, is honored to be asked. Give it a try :)

I have emails out to a couple others, but... her and one other helped me though a very ugly situation with the Dept, even though neither worked for the school at that time.

If you're worried she might give a negative rec, then probably best not to ask. Or, you could simply call her and ask if she'd be comfortable doing a rec and you can make clear you would prefer she not refer explicitly to the "ugly situation."

You should ask for the recommendation.

Of course u should ask!