I think Kraft's in a tough spot to be honest. If I've read things right, he has no recourse similar to what Brady has. Brady will continue down the appeal track, hopefully reject whatever Goodell rules and bring it to an independent arbiter. Kraft doesn't have that option, as a league owner. His only options: compromise with Goodell, or sue the league.
As much as I'd like to see him sue, it's unprecedented (in the non-Al Davis world) and he'd be making a lot of enemies around the league. I don't necessarily think that's a bad thing, but it's bad for his business and would be a massive circus show, I don't think the nuclear option is realistically the best way for him to go (even if we'd all love to see it).
No, I'm fine if Kraft negotiates and gets penalties reduced (the 1st rounder HAS to be returned though, that's a dealbreaker for me), and the Brady/NFLPA proceedings are the venue to get names cleared and maybe even bring up some dirt against Goodell/Kensil/Vincent/Wells.