Just leave it as it is now.
If people want to kite a giant enraged turtle around a lake for an hour after it enters hyper-mode, that should be a viable strategy. If people hate themselves enough to fight a matamata or uraganite for two hours and not kill it, that particularly cruel method of self-punishment should be available to them. Implementing a timer would just homogenize all the fights and possibly even force certain monsters to be adjusted to conform to the new timer.
