In my game you can start re-training units after one turn in a newly captured city so that isn't really an issue.

Mercenaries obviously help in raising powerful armies quickly but they are relatively expensive anyway and would be harder to recruit if sacking did not boost your treasury funds. They also form a pretty fundemental part of the game and so I whilst I think the whole system for how they work needs to be reviewed I would not want them removed completely from the game just to prevent an unrelated player expliot.