Doctor Who showrunner Steven Moffat answered some questions on whether we have seen the last of The Master. The answer he gives suits me fine as that is how it used to be in the Classic Series and everyone was fine with that explanation back then.
"I always rather enjoyed how they handled this problem when the wonderful Anthony Ainley was playing the part in the 80s."
"He would get killed, definitively, at the end of every encounter with Peter Davison and Colin Baker. And then he'd turn up at the start of the next Master story with roughly this explanation: 'I escaped!' Suits me, I'm fine with that!"
"Supervillains don't die, do they? I wouldn't trust anything about that character's ability to lie down and stop breathing."