Hi clinicman
Feeling guilt is pretty normal around these here parts

A lot of us don't cope well with lots of guilt, which makes us have weak boundaries, and people with BPD, having no boundaries, find a nice fit, at first. Except no one likes a doormat, least of all someone who needs and (deep down) wants their partner to have firm (and gentle) boundaries. It's exhausting, and takes a lot of skill even in the best of times before the resentment torches it all down.
Disrupting the lives of the kids is hard, although having been out of my BPD marriage for many years now, I will say that my S15 is doing a thousand times better than if we stayed. When you stand up to a bully, kids notice.
It is the hardest thing to try and protect them from someone they (want to) love.
The guilt is normal, and makes you human, and it's probably a good idea to get to the bottom of it to see what it's about. Chances are you were raised to think that your job was to make things better for others, at the expense of your own self-care. It can take time to realize you deserve to be loved and respected even when others disagree.
How old are the kids? How are they doing?