This is a good subject, and one I have struggled with.
The scripture that sealed the deal for me was Nehemiah 4, when the Jews were experiencing violent opposition (as they were rebuilding the walls of Jerusalem)...
They were ordered to place guards...with weapons, to protect themselves.
IOW, self-defense is “ok” from a Biblical perspective.
Neh 4:13 Therefore set I in the lower places behind the wall, [and] on the higher places, I even set the people after their families with their swords, their spears, and their bows.
Don’t struggle. Bonhoeffer was right about this much, “To do nothing in the face of evil IS evil.”
The Bible and self-defense
http://www.wnd.com/2001/11/11783/