I've basically agreed with everything you've said so far. We don't really know what he did so it's hard to judge one way or the other. I don't know that I'm willing to give the team or MLB the benefit of the doubt though. Especially after the All Star game ********. I also think it's really rich for the team and MLB to pull this now when everyone knows who Alomar is. Dude has had scandals and a poor reputation chasing him for years but this current regime employed him for 5+ years anyway. I'm actually amazed it took this long for something to happen.
Without knowing what happened exactly (without any criminal charges my guess is it isn't anything worse than the other things he's done or been accused of doing before) the best move, IMO, would have been to just let him go but keep his name on the Level of Excellence. Yes, they can have the reunion but he's the only HoFer we have and he had some huge hits, perhaps the biggest in franchise history. It's sort of like having a Rolling Stones concert without Mick Jagger. You could do it but it'd be stupid.
And yeah, they can't literally erase him from history because it's impossible. But if they had a time machine I wouldn't put it past them.