Her mind controlling the Stormtrooper didn't bother me because it was setup that they are indoctrinated from birth. You know what did bother me? The shameless killing and execution of Stormtroopers in the movie. The movie just established that apparently most of these people are kidnapped as babies and indoctrinated as Stormtroopers, then they show Finn turn away from his brain washing and try to escape. So now that you've humanized Stormtroopers why would I be so enthusiastic about these terrible deaths the characters inflict upon them? Why would I jump in glee when Chebacce hits them with his Bowcaster so hard they fly? Instead, I'm thinking "geez, I hope that guy wasn't secrelty a good Stormtrooper."
Now, if they were just Space Nazis I wouldn't have that problem but now I do.
I think the point is that Finn started out relatively good before being forced into being a Stormtrooper. You can clearly see that a bunch of these guys don't give a shit about gunning down innocents without even being told. The real-world parallel is the police officer who steps forward to out his corrupt buddies while they call him a traitor and turn on him (which happens to Finn).