Well it does benefit the club in certain circumstances. For example certain players can be toxic either directly or indirectly. The direct part is self explanatory. However the latter can happen as well especially in a highly pressured/high stake environment such as football is were a big chunk of the salary is tied with club performances bonuses. You see, every club has a wage budget. If there's a player who, for one reason or another is not pulling a shift then that would have an impact on the club which in turn will have an impact on the team's performance. A well run club will always make sure to get rid of players like Jones. They might give a second chance to a top talented/injury prone player but Jones is not one of them.
If you ask me I have a feeling that the club is actually trying to get rid of Phil. Leaks like Ole being shocked that someone gave Jones such long contract + him not being taken to the tour are clear example of the club wanting him out. No one can say whether Jones will take the bullet or if the club is ready to take it to the next level though.
Toxic... Lunatic. Semantics...
Jones isn't toxic as far as we know, so there's no point to fire him in that case.
I'm not sure you can just "save" money by not paying bonus tied wages upon firing. Regardless, I imagine there's very few bonusses he'd be getting if he's injured and barely plays anyway...
If he decides to mutually end his contract so he can move on a free or if we manage to sell him on a for a small fee you might end up making a loss, which again, why risk it if Jones isn't being a nuisance.
And all this is under the assumption that you know he's going to be near useless while he's carrying the injury, which is just talking in hindsight.
Basically you're talking about this stuff in a generic sense when that's completely pointless 'cause we know who the subject is.
And btw, Van Ginkel at Chelsea had a similar disastrous injury spells at Chelsea and was given a one year extension after his contract had run out. So this idea that having an injured player on the books or something is "exemplary of the current state of Man Utd", which I've seen mentioned a lot here in this thread, is silly.