There are two examples of phaser-type weapons actually acting very much like transporters: in VOY "Macrocosm", they with minor modifications deliver nanomachinery to the victim, and in DS9 "Siege of AR-558", they either deliver poisons or then generate those in the victim.
It could be argued that this is the simplest, bluntest way to use a phaser beam as a weapon: it delivers something that messes up the victim when popping back to the un-phased realm within him or her. With stun setting, it could be an agent that overloads the victim's key systems one way or another, but has little effect on the rest of the body. No need for accuracy, no need to spot blood vessels let alone specific molecules or molecule types within. Just impregnate the victim with a potent knockout drug, enough of which gets where it needs to while the rest doesn't create permanent damage and harmlessly dissolves soon enough. "Kill" could be upping the dosage, and would have little or nothing to do with "disintegrate". And that, too, would match the onscreen evidence of repeated stunning being fatal (yet apparently if and only if performed within a short span of time).
Alternately, the phaser beam could transport an electric charge to the victim, essentially acting as a wireless taser.
Timo Saloniemi