I think that Fred, in asking Wesley for help in Supersymmetry, was simply desperate for revenge. Yes, she *obviously* made the wrong decision in wanting to send the prof. to a hell dimension, but if you think about how evil he is and what he put her through, you can see how a desperate Fred would feel. The minute she found out what he had done she knew she could not do it alone, and due to Gunn's heroic image (fighting crime on the streets, helping the helpless) she knew he would not help her, and she didn't want to 'corrupt' the image he had of himself - a capeless superhero doing what he thinks is right. However, Wesley had already proven himself to be something of a dark horse, he was basically straddling the line of good and evil. He kidnapped Angel's own son and was a contributing factor for Connor to be sent to a Quor Toth, and to the majority of Team Angel his motives were questionable.
I’m not going to say what they did was a good thing, but at the time Fred figured if she really wanted revenge she needed an accomplice, and Wesley was the one she turned to. Gunn she thought wouldn’t do it for the reasons above (and she wanted to protect him), Angel wouldn’t help her because he’s Angel, Cordy was out of the picture and Lorne isn’t really the type of person you would even consider in such a situation.
The main thing is, Wesley did not have to accept her proposition. Instead, he says, “Vengeance. Sounds good,” and does nothing to dissuade her. So, the thing about Wesley’s “mortal soul” is that in the end it is his decision, and he helps her with the spell. Also, if we just go to when she’s about to go into the building, he says, “I’d ask to tag along-“and she replies, “but you know what the answer will be”. Ultimately, she figures she wants to do it herself and doesn’t want anyone else involved.
Also, by season 5, Gunn is over Fred, and likewise (romantically, anyway) so I doubt he would get himself lawyerised because of her opinion of him. He says in ‘Shells’ to Wesley, “It was just a piece of paper. I was losing it. Everything they put in my head, everything that made me different. Special.” I think it was more he didn’t want to go back to being just the muscle, he wanted to be useful in a way no one else was, to have an understanding of the law. If anything, I think W&H is to blame, not Fred.