Do you get it? He was a bad guy and he gets turned into what he hates, oh the irony! There's no ethical implications for turning someone into a new race because he was a bad man. But asking the Dr to hold a pistol to a war criminal (as opposed to the 200 year slave family) and you've got some srs bsns right there, that's where the real moral crisis are with guns.
And the one right after, an allied officer is stood next to the Dr and he basically tells him to piss off because he's carrying a sidearm because guns are real bad. Not only that but it starts out with UNIT (UN anti-alien team basically) moving into a plant to search for aliens, naturally securing the civilians whilst they search and more than once they get likened to storm-troopers by the Dr's companion - essentially for following a pretty basic proceedure and using military protocol.
It's really just the conflicting preachy [censored] that bothers me, I'm trying to think of some more examples because there are loads; don't even get me started on Torchwood either, good God.