It seems to me they did wait for the offseason, unlike what you said. They saw how the season went, and rewarded him. Hence, it was nothing like the Jauron or Fitz deals that occurred in mid-season.
Freddie was playing like a beast and he was being grossly underpaid for it. At the time, everyone knew that and agreed. He deserved a raise, and the Bills came through for him. I think that speaks highly of the organization, and I'm betting the players took notice of that. It's a good thing.
They could have waited yet another season before rewarding Freddie, but it's likely he would have been unhappy and maybe even held out in the preseason. Just because, in hindsight, you have the benefit of seeing the next injury and Spiller's performance doesn't mean everyone knew that would happen last offseason.
This isn't even in the same stratosphere as the Jauron and Fitz deals.