Urias was suspended far fewer games and was never charged with anything. What that suggests is that Herrera's actions were more horrific - 4 to 5 times worse, perhaps - even though he was ultimately not prosecuted either. And many victims of domestic violence stay with the person who abused them. In Herrera's girlfriend's case she is likely dependent on him both financially and, also, quite possibly, in order to remain in the United States.
More importantly however, Urias is a good player. If anyone still thought Odubel was a good player either he would have been traded easily, just like Osuna was, or the Phillies would have been a lot less concerned about moral and public relations issues.
It was foolish of them not to put him on the 60-man roster last year. Whatever he may or may not have left, he needed to get work. He's set up to fail now, having not been a good player for almost three years, nor seen a live pitch for two.
But his "second chance" is that he still gets paid and he's still a member of the organization. Even if he gets the invite I doubt he will get enough meaningful ABs to make an impression, nor should he really, given Haseley, Quinn and Kingery need them just as badly (Miller and Cutch can probably be more limited, though they may actually want to test Cutch harder this year).
The Phillies aren't allowed to just say, "we're cutting this guy because of what he did." If they could, and did, I'd have no problem with it. If that ruined his career or cost him money that would be more complicated - such "no tolerance" approaches can lead to both financial hardship and repeat offenses that make things even worse for the abuser's victim (and/or children, if they have children). That's not really the case here, however.
Basically, Middleton has handled this exactly as well as every other important decision he's had to make in the past two years - the fact that it's never clear who actually get to make the decision, and the firmness with which it's being made.