Just to be nit-picky, Gunn didn't slit the professor's throat, he snapped his neck. Still nasty though.
I was always torn when it came to Supersymmetry. On the one hand, I can completely understand Gunn and Angel's stance when it came to Fred seeking vengeance against her professor. A major theme in the Buffyverse is that vengeance/revenge-driven “justice” will ultimately undo and/or change you irreversably. We see it when Buffy goes after Faith in Grad. Day Pt. 1 and then again when Willow goes after Warren in Villains; in both instances people around them expressed concern over what their actions will do to them.
So with this line of thinking, it’s definitely understandable where Gunn was coming from. Frankly, if my partner wanted to kill someone as revenge for previous trauma, I would do everything in my power to stop him, including doing the deed myself. I would rather add more damage to myself than to see him shoulder guilt that huge.
On the other hand, from Fred’s side of things, she does have every reason to want bloody-thirsty revenge on her professor. God knows the horrors she endured in Pylea and to finally know who sent her there and why is huge for her. For Gunn to take her vengeance away from her, even if it was to save her, is not right.
That being said, I don’t think Fred and Gunn fell apart after all this because he took her veneange away; to me that’s oversimplyfying things. I think they fell apart because Fred couldn’t bear looking at Gunn in a differet way; she never met the street-thug Gunn, the violent, out-of-control death seeker. She knows only the good Gunn, the noble and protective Gunn. Therefore when she is forced to watch him murder someone, it changes her whole view of him; in addition she carries huge guilt because he became a killer for her and this is what ultimately drives them apart.
