I don't see how concerns about injury are a taboo topic, nor Manny's *******ishness.
If they believed that Bay's knee was only worth 2 years of investment that's their perrogative. What isn't mentioned with the report are the implications of him having bad knees. It isn't just that he wouldn't produce like he does now, or that his injury might cause him to miss games over 4 years, it's also that his defense would get considerably worse and it was bad to begin with.
I don't see any reason for a topic like his knees to be withheld after he's signed with someone else. I don't know if it was the FO releasing this info, but if it was (and if it is true) then the only people to whom it appears conspiratorial are those who disagree that Bay can be replaced.
It seems to me that the same was true of Damon, Pedro, etc., and many of the people who questioned letting go of Pedro, Damon, Cabrera, etc., snatched onto any explanation of "why" as some sort of FO plot to tarnish players that they didn't even really want for the asking price on their way out of town.
Why would this team do that? What interest do they have in getting a reputation as a team that kicks FA stars away in disgust? I don't think that's the reputation they have in the league.
I can personally make arguments about each of the players you laid out above and why it was in the Sox best interest to let them go. Whether or not the reasons were infered on my own or through propaganda doesn't really matter; if they're right, they're right. If they're telling the truth about things then I don't much care who is presenting it.
Was Manny a douchebag who had to go? Yes. He wanted to leave for years, his contract was going to be up soon so he could be moved, and he quit on the team according to the players, near the end, and he got in a confrontation with a Sox staff member. He had to go and the stories are going to follow him.