One way to lower loyalty is to give them really bad governors. Gather up the guys with any unhappiness vices, low piety, little dread and make them governors. Governors with "hidden" vices are good - they ussually cause loyalty to plummet if the vice is revealed. Use very low valor spies and assassins for failed assassinations and loyalty trials of your governors, each time they fail their loyalty will go down and they may start picking up vices like "paranoid", etc.
If you keep killing all the rebels after the battle, you start piling on unhappiness vices. At first you just get a little dread, then the dread is accompanied by unhappiness.
EDIT: The other thing to do is to keep killing prisoners while you are still on the battlefield. Again, the first time gives your general a little dread, but the more you do it the more unhappiness he starts piling on.
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