I'll let one of the old school crowd address the significance of the Master, but the short version: Time Lord nemesis.

what would it matter if he killed Saxon or not?

It makes a huge difference. The Doctor was directly responsible for the obliteration of his people. Now, he finds out that someone is left alive. (That someone turns out to be, as I said, his greatest nemesis.)

It's genocide, part 2, plain and simple. It may be necessary, considering the threat the Master poses, but it's still a horrible consequence.