Can or should a Buddhist defend themselves physically? If someone is attacking you to kill you should you defend yourself? Would it be ethical to kill an intruder coming into your home? If not, how did the bushido  samauri warriors justify it? We're they wrong?
If someone is attacking you to kill you should you defend yourself? ...


I think yes, you may. Our religion has never stopped us from doing that. 


  Would it be ethical to kill an intruder coming into your home?


you may stop an intruder forcefully. Our religion has never stopped us from doing that. 

But for me, being Buddhist, the answer will not end there. Both (two above lines) questions are based on teaching of Ahimsa (not to injure). If it is so then it is important to know how we interpret this teaching. Following are some of the points we can consider- 


Buddhism is a religion of principles and not rules. (yes there are rules as code of conduct, but it is not religion of rules). It teaches you basic principles and you are expected to make the decision on basis of that according to the context.
Buddhism is religion with "Metta" (unconditional love). You even are expected to love your enemy. But you are not prohibited from defending yourself. 
Ahimsa in Buddhism is not the same as it is in Jainism. 


These are the points in short based on which I said you can physically defend and you are not stopped by Buddhism from doing so. I don't want to say that you should (or even you can) kill. But you may defend. Dr. Ambedkar's discussion on Ahimsa is very enlightening in this regard. You can find it here -The Buddha and His Dhamma, Book 4, Part II, Section 3. It is a good read and the best part is it covers the whole debate in two pages. I also found this article interesting discussing the same point.