That's a theory I came up with in a previous post. Other people elsewhere have probably had the same thought. The fact that the Doctor who was shot started to regenerate was the biggest point against it being a ganger Doctor for me, until I realized that it could have been the ganger who got River's regenerations.

Other possible fun bits of dialogue that could actually be clues:

[River, on the idea of two Doctors]: That's a whole different birthday. (Maybe she meant it.)

[Madame Kovarian]: Fooling you once was a pleasure. Fooling you twice, with the same trick ... that's a privilege. (Maybe that's Moffat talking to us about how he's going to try to fool us with the same ganger trick he used for Amy. However, I don't think she really fooled him the first time. I think he suspected Amy was a flesh duplicate from fairly early in the season.)

I still can't shake the nagging feeling that the ganger thing is a red herring. But the evidence seems to point to there being two Doctors in some way, and the ganger is the most obvious method to explain that. Doesn't mean it's the only possibility though.