Primarily the opinion that 'zombies are just sick people' is held by Hershel. Reasons why Maggie (and the remainder of the farm group) go along with this could include:
a) There is no proof yet that the opinion is incorrect,
b) They have loved ones who have become zombies who are held in the barn, and
c) Hershel is the dominant personality and leader of the group
However Maggie clearly can see that the zombies are dangerous, and probably seen that they can and will kill people. If Maggie had seen another (alive) person attack Andrea in an attempt to kill and eat her, its possible, even likely that she would defend her with everything up to lethal force.
So in situations where she is defending herself or others she might reluctantly use force, but that is not entirely inconsistent with preferring to keep zombies alive and captive rather than killing all of them - in the distant hope that perhaps the plague's effects can be reversed.
She is disgusted by the death of the zombie in the well, but it was not clear to me that this can only be put down to her being in outright agreement with Hershel's opinion. The death of the zombie was particularly grisley, she's as disgusted by them as anyone else, and she knows her mother is in this state in the barn. As well as possible sympathy with Hershel point of view, she is might be nervous of Hershel's reaction should he find out what Rick's group did, not wanting Hershel to cast them out of the farm. In addition she is finding herself attracted to Glen, and (as expressed in later episodes) she is afraid for him when he repeatedly puts himself in dangerous situations like being lowered into the well. Her reaction could be any or some combination of all these emotions.