In Dinosaurs on a spaceship he kills the bad guy (admittedly a really, really bad guy), and then in Mercy he is initially keen to kill bad guy but then has a change of heart. Seems a bit out of character. Is the Doctor becoming callous in his old age or what? Or is this leading somewhere? Any thoughts?
That was badly scripted IMO. But the general idea is that he isn't spending as much time with Amy and the Roman and so he's getting revengeful and angry again - because that's what happens when he has too much time on his own.....
That sounds about right. Amy in particular seems to ground him a bit. A previous episode implied he had aged a couple of centuries while away from Amy, seems like all that time alone left him bitter.
Dr Who is a kids show, so we can't unravel it too much - because it starts unraveling very easily ... :)
Also, if you've watched the classics, the Doctor has had moments where he's almost killed someone, or he has, or whatever. This isn't a just new thing. It just depends on what's going on at the time, the story. He's not infallible. He's a madman in a box. :)