I wasn't a fan of the moral dilema personally, or rather the way it ended. I'm getting kind of sick of episodes where The Doctor has to make a moral choice (Free or kill the Dalek in 'Dalek', Wipe out the humans and Daleks or do neither and let the Daleks kill the humans in 'Parting of the Ways', etc.) and it ends up sorting itself out before he decides (Dalek kills itself, Rose kills the Daleks.), it always strikes as being written into a corner so as not to make The Doctor feel guilty for another murder.
I don't mind The Doctor pointing a gun at another living thing so much though, I actually thought it was quite in character for him assuming they're going down the route of the Valeyard. Or if you take note of the murders he's committed in the other episodes of this series alone.
I do think Amy was being a bit self righteous though, she herself killed the alternate Madam Koverian last series, there was even an entire sequence of dialogue in which she claimed Amy would save her because The Doctor would, and she basically says "The Doctor isn't here so I can murder you all I like.", sure she immediately regrets it but she doesn't even bring her hypocrisy up during her exchange with The Doctor about finding an alternate method. And as other posters have mentioned, she would've killed all of the Flesh Gangers from the start if she had her way.
Not my favorite episode of this series (Though I happen to think the previous episodes are absolutely top notch.).