I think that the difference is already taken into account in the amount of damage. For instance, if a phaser shot takes you 10 wound points (very low setting, rather easy to heal), the same amount of damage can be reached with at least three punches from an average human (and one particularly successful punch from a Klingon). This seems rather comparable.
Similarly, if a single phaser shot puts you Incapacited, you'll have to be pummeled consequently to reach the same Wound level (let's say, four or five Klingon punches and a dozen from an average human) - and, as ImperialOne pointed out, you can be in a very bad shape after such pummelage.
I think I'm definitively gonna settle for the house rule of requesting a Stamina Test everytime a player loses a wound level to stay conscious - just have to adjust a correct TN (don't have my books at hand for the account on being at work ;)).