A Couple of things.
I believe Michonne followed the other zombies to the prison and that is how she found it. I mean if you look there are now more Zombies on the outer gates then there were a couple of episodes ago. That means they are flocking there
The Red zone they are talking about could possibly be where the prison is. This could be the reason the people of Woodbury haven't ventured over to the Prison.
Also the reason being Glen not shooting Merle with accuracy. Walkers are slower and kinda shambling along. It is easier to target and fire on a walker. But Merle on the other hand as shown by his fight in the zombie ring and his fight with Michonne that he can move fast when he wants to.
I don't know if the next part is spoilerish or not but....According to the comic, Michonne was the one the Gov. did the rape train on correct? She doesn't seem to be a sympathetic character in the TV story line.
What if they flip that around and have Merle state to Maggie "If you don't tell me where my brother is well....I can't be held accountable for what will happen next" Maggie says screw you and then Merle walks out of the room shuts the door behind him and all you hear is Maggie screaming. The Merle nods with a little evil grin as one of the Cronies pass by him and goes into the room with the other dude that was already in there. It is implied but not shown or said. Maggie is a much more sympathetic character and would drive people to hate Woodbury.
Just my thought. I could be wrong and they wont show any of that.