What should the Indians do with Chris Perez? Simple. Rehab his shoulder and pitch him. That's it. Don't do anything until Major League Baseball, or the legal system, says you have to. There is no reason to and they do not have grounds to do anything else.
Perez, like all Americans, is innocent until proven (or pleads) guilty. Even if it appears that the situation is headed that way, the team cannot act until the process is over. Also, a player cannot be disciplined by MLB until the legal situation is resolved. Perez has been charged, there are mug shots and a police report that does not sound good. There is plenty of smoke to this fire, but the team can't act until the fire is put out.
In the mean time he'll rehab his shoulder and eventually return to the 25-man roster. It might be awkward, but Perez already faces his share of detractors every time he takes the mound at Progressive Field. What's one more issue? This is a misdemeanor charge. It's embarrassing, but it's a minor offense. The team should not over react. Fans will react however they're going to react, heck, some of them boo Perez as soon as he goes to a 3-0 count on a hitter. Of course they are not going to let a chance like this slip away! I just ask that you keep some perspective.