I think I may just have believed this possible - I mean handing villains over to the authorities without necessarily asking too many questions is fairly Who-ish - but, you are right, the moment an issue is made of it, it becomes a false dilemma we know is going to be resolved without the Doctor having to both make a choice and face its consequences.

Wikipedia says the original outline of the episode is about how the Doctor constructed Rose in advance as his perfect companion. On the whole I'm glad we got Boom Town instead.