If you stun your enemy, great, they're temporary unconscious. If you have the personnel, you can now watch them, or carry them to a detention location.
Otherwise when they wake up, they are able to oppose you again. If your on a fast raid this would make little difference. But in a protracted war, if you merely stun your enemy, you screwing yourself over.
Add to this the psychological factor, if a enemy truly believes that the worst that will happen to them is that they will be stunned, there will be no hesitation in charging your position, or your raiding party.
A dead enemy can't keep coming at you. When Starfleet uses phasers and torpedoes on a enemy ship, they are killing people by the hundreds, and in a major fleet engagement by the tens of thousands.