The Ben Thatcher example is something done on the field. And I'm not talking about disrepute - it's about employment contracts. Agbonlahor's contract with Villa has an implicit (and probably explicit) expectation of a professional approach to training and fitness, to ensure he's available for games and capable of playing in them. Clearly he's already been disciplined this season by the club this season and demoted to the U21s/suspended. If as part of the last discussions (his 'warning') he was told of his responsibilities and accepted that, or committed to a specific fitness plan which this can be shown to have broken, he can be deemed in breach of contract.
The real reason it's rare, is that clubs will always look to sell to recoup some money; the examples of sacking therefore being serious criminal offences where there is literally no sale value and the player has blatantly breached his contract (if he's imprisoned, he really isn't available to play). But Agbonlahor is getting pretty close to unsellable and is not very good at hiding his unprofessionalism. It would be a bit of a landmark case, but I think the club have grounds to pursue it.
I understand what you are saying, but surely on the field behaviour is equally applicable to a player's employment contract? As you say, a player is expected to offer a professional approach - which means not deliberately trying to put an opposition player in the hospital.
I agree that clubs want to preserve their investment - otherwise Sterling would have been out on his ear for some of his off-field antics with us. But I feel my point stands: trying to use Agbonlahor's behaviour as a pretext for breech of contract seems tenuous at best.
As I said - perhaps Bernstein wanted to pursue this avenue but was overruled by somebody believing they might yet get some money for him. On the other hand there aren't that many people in the club who would have been able to overrule him - which gives some insight into the mess the club is in.