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It would seem that the front office knows more about McDonald than they're letting on, hence the hasty decision to separate him from the organization. One would hope that's the case anyway and this isn't just a knee-jerk reaction to more bad press. This is also decidedly more negative press, carrying rape allegations and a hospital visit by the alleged victim, and things are already not going great in Santa Clara on a number of other levels as we all are well-aware.
No matter their intentions, the 49ers have made their decision and the best that they can hope for is that it sends a message to the rest of this team that maybe you don't get the benefit of the doubt and the allowance of "due process" if you make the team look bad. Ray McDonald was definitely making the team (the struggling, drama-filled team), look even worse than they already did on and off the field and regardless of his role in the most recent events that took place, his head was on the chopping block and an example was made. There's certain to be many new faces in many new places for San Francisco next year, and messages are getting sent now about how business is intended to be run. At least, that's what Jed York is messaging to the world right now anyway.
It seems unlikely any other team would pick up McDonald, though still a talented player, until his newest legal matters are resolved. Given the pace of his last run-in with the law, that would project to be well after the postseason has started and probably after the final games are played this season. Should things get resolved more quickly and again McDonald is not charged, McDonald would be free to sign with any team. This of course would make the 49ers look completely reactionary and foolish, not out of the question with all that's going on right now, but given the timing they should not have to deal with that press for at least several months.
If McDonald is found to be in violation of NFL conduct, and more importantly of United States Criminal Law, then he'll either serve a suspension or jail time and could likely resume his NFL career elsewhere, depending on the seriousness of the charges. In a morbid sense, this is what the 49ers are hoping for at this moment. Few details of the situation have emerged that shed any light on what McDonald is being accused of and the tumultuous relationship between he and his significant other means truly anything could be possible.
Finally, it's important to note that Ray McDonald ended up never getting charged for the domestic violence situation that came up at the start of the season, but never was he truly cleared of his accusations either and no story really came forth. The big reveal of that storyline was that the 49ers had San Jose Police officers on their payroll and it was becoming evident that their involvement in that case clouded things significantly as to whether McDonald was going to be charged.
It becomes a legitimate question now, in light of the 49ers recent decision with McDonald, did the team know that he was not guilty at that time because of their involvement with SJPD or did they know that he just couldn't be implicated because of the evidence (or lack thereof) they presided over? Now that the SJPD is prohibited from working with the team, McDonald certainly didn't have a team-friendly officer to call in this situation and help sort out the details. Knowing this and knowing whatever they knew about the first incident, the 49ers may know that this story is going to get a whole lot worse. It may also mean they knowingly played and protected a player they knew to have broken the law, an ugly but not unrealistic concept considering the stakes in play for this year.
For the team that bellowed the question of who could possibly have it better than them, things just seem to be getting worse and worse.