Hi reluctanthusband,
living with a pwBPD does require sometimes compromises but on the other hand let's not forget that often with a compromise no side is happy. Besides a person prone to b&w thinking will rarely be even content with a compromise.
The new church she is going to is great(honestly it is) has all sorts of loving people(for now) and great programs and is closer. But I am involved in ministries at the other church and love the people there(A lot of active and former military).
Should I reconsider my decision to leave my church? I do not support her leaving, but am not going to stop her from going to a good church even if I think the reasoning is wrong.
It is her decision what to she does. I would just be careful not to severe any link to a support system that has helped you in the past and kept you sane. Leaving it will make you more vulnerable. Doing always the same what your wife does makes your wife more prone to anger outbursts.