*They were kidnapped and disarmed
Disputable. Andrea had just fallen unconcious and is clearly very sick. They were found with two walkers near the crash site. They were picked up and disarmed. Kidnapped is a hard sell. Being disarmed is not a bad strike.
*They were not allowed to leave, repeatedly, for one reason or another, they were not allowed to leave, this was enforced by a guard.
When were they actively denied? Tell me. When were they refused to leave. They were told that they could not leave at night, that is all.
*Michonne's sword was on display in the Governor's house, not in an armory or shared location, in his house.
So the Governor is a kleptomaniac. That makes him evil?
*The Governor will not reveal his name.
I won't reveal my name. Does that make me evil?
*Merle is in a leadership position. Merle was unstable and racist in the first episode. Andrea knows what happened. That reflects the governor's priorities.
We saw Merle for all of half a day during a very stressful incident. His current actions are not the same as on that roof. Notice how polite he is being with Andrea. And that is by choice no less.
*Merle got in her face while discussing the "simple" issue of letting Michonne go. he was clearly giving private instructions to a guard.
Assumes facts not in evidence.
There is not a shred of evidence available to Andrea that the Governor is evil. The only definitive evidence we see are situations or details that neither Andrea or Michone know of.
You are letting your increased knowledge of the Governor color your opinion of Andreas reactions. They saved her life and offered her sanctuary. They have been polite and helpful to her.