It's really something you have to pray about and decide for yourself.
Regarding the passage in Matthew above, it's easy to mistake stuff like that, but you have to recall that "eye for an eye" was revenge, justice, if you will. If someone stole from you, you took back from them in equal amounts. It was not about self defense, but about vengeance.
The 6th commandment is also messed up due to years of inaccurate translation. The original word is more accurately translated 'murder', not 'kill'.
The simplest way to think about it is this - do you really think God would not have you stop someone, at any cost, from harming a child or a woman? It seems ludicrous to me that someone would think God would want you to sit idly and not stop someone from killing an innocent.
As written by C.S. Lewis: "he's not a tame lion..."