Wasn't Gwen's father executed for allegedly using magic in an earlier season? It's been awhile since I watched the old seasons, though, so I might be wrong. Did she ever find out he was set up? Maybe she thinks her father might have used magic.
I think Gwen is confident that her father was innocent, but she probably doesn't know what happened. Gwen knows, based on what her father told her, that he didn't know he was getting into anything involving magic, but did know that the situation was fishy enough that he was afraid to tell her about it. While innocent of deliberate involvement in sorcery, the blacksmith's mistake was to allow the lure of money to make him disregard his own doubts about a client. So Gwen knows that a sorcerer got her father into the situation that got him killed.
Gwen does know that he was falsely accused of conspiring with a sorcerer, and died for it. This combines with her own two close calls with nearly being executed by Uther for sorcery, and the ravages of the witchfinder framing everyone he could, and she should have a deep sympathy for the falsely accused and a strong interest in never seeing anyone falsely convicted of any crime.
But have her experiences ever taught her that those with REAL magic aren't necessarily evil? She saw the boy Mordred as an innocent, but wouldn't know he had magic (she wasn't there when he exploded the mirror). She did see the magic she believed Merlin's friend Will conjured to help in the first battle of Ealdor, so that's something. I can't think of anything else. Oh! The first time she was falsely charged with sorcery, she might understand that someone had healed her father with magic, but she may not have understood that, and if she did she might not be as grateful as you might think given how it turned out. With as many horrible things she's seen caused by magic, it would be hard to blame her for remaining in the sorcery-is-evil camp.