Really there are a lot of scenarios and storylines which could be used as a way for her to seemingly "kill" the doctor, but not actually be killing him.
It's quite possible that she kills him and he regenerates, although this won't be happening anything soon in the actual show due to Matt Smiths appointment . It would be more likely that this part of the story is alluding to an event that occurs a long long time later in the mythology of the show. In the final part of the episode when he said 'I could kiss you' and she replied 'not til you're older' (or words to that effect) alludes to the fact that her first meeting with the doctor (from her perspective) won't actually happen for a long time for the Doctor.
That is of course assuming its the doctor she kills, the only info we have currently is that she kills a good man, the best man she has known. Which wouldnt necessarily mean the doctor, indeed if one was to be pedantic about it, technically the doctor isnt a "man" and as such wouldnt count as either a "good man" or "the best man".
Tbh the fact that she said those words while her/the camera/the scene focused on the doctor implies otherwise. I bet money that hes the one she kills, its the most logical outcome from the facts we've been given. You just have to put the pieces together