The Doctor pretty clearly can't be held responsible for any of Amy's actions up until the end of Day of the Moon, which is the bulk of that time. Not to mention, at 5 months she should be visibly pregnant which she clearly is not. There doesn't even appear to be an actual fetus physically in her womb at present to be harmed by anything.
Not to mention that, if she were pregnant, a certain other female bodily function would most likely have been suspended, and I'm sure she would have noticed that (possibly its absence and then late occurrence is what prompted Amy to tell the Doctor "I'm pregnant" and then "I'm not pregnant").
Of course, that's a little hard to work into a show watched by children (and more importantly, the Daily Mail
