Ethical disassembly?

so i was watching terminator salvation for the first time today. when they catch marcus and say they are going to disassemble him, i had a thought of ethics. if you were in that situation, where you had been at war with a machine race for years, but you are faced with "killing" a being that is part human and part machine out of fear for your own life and the safety of your kind, would you do it, and would it be moral?