I feel for the guy, and it's not like corporate shenanigans haven't happened at Rooster Teeth before (Ray's original twitch channel being taken for use by the whole company, which really soured him on the company for a while and might have contributed to his decision to leave). Maybe to him the changes to RWBY and the "shutting out" of Sheena did feel like betrayals. And maybe I'm biased for having been a fan of Rooster Teeth for so long, but frankly I don't see any of this as a real problem. It sucks for Shane and Sheena, but an artist is always going to argue for "artistic integrity" and even more so when they were close to the showrunner.
It seems to me, trying to sift through all the baggage in his letter, that the big wigs at Rooster Teeth felt the best way to honor Monty was to ensure RWBY be a success, which certainly has merit. Shane, meanwhile, seems to believe the best way to honor Monty is to perfectly preserve every iota of anything Monty that already existed, including having Monty's wife there for the rest of the ride, driving the show as she thought Monty would have wanted. That also has merit, but the two ideas are obviously mutually exclusive; Sheena may have had better insight to how Monty wanted the show to go, but Miles and Kerry who CO-WROTE the show would no doubt get tons of resistance from her for any changes they might try to make, which obviously is no good. So it makes sense to me, harsh as it is, why they'd want Sheena to stay out of production.
I can't speak for the guy's friendship with Monty, or Monty's relationship with Sheena, but it's not like they were Monty's only friends. He was friends with Miles and Kerry and many other people at the company. The point is, it sucks that he got fired, but I have a hard time believing he was the only one who cared about Monty's vision. It's just much easier for me to believe that he had a strong idea of what Monty's vision was, and when other people started to stray from it, he couldn't reconcile that with his own hang-ups. It's not his fault; it's not anybody's fault. Someone died, tragically, unexpectedly, and dozens of others were left to continue on without him. Eventually those left go their separate ways, trying to honor the memory of the deceased in what way they think is best. That's just how it goes, sadly.
EDIT: It seems the people over on the RT subreddit [https://www.reddit.com/r/roosterteeth/comments/4j20kc/shane_newville_an_open_letter_to_all_who/] (hardly an unbiased group of folks, but eh) have much less regard for what Shane is doing than I do, and I don't have much to begin with. But they make a lot of good counterpoints, the biggest of which is Shane's manipulative use of his friendship with Monty to make him seem like a victim while disregarding all of Monty's other friends at RT as just part of the RT collective. Can't disagree with them on that, really.