I´m new to whole modding thing, but so far, no one seems to react, thus I´ll give it a try.
To do so, you´ll have change one model for another, so it doesn´t matter, wether you change only head morph or whole race, gender, what so ever.
If its suppose to be the boss fight, it could be handled by cutscene and plotflag, that will stop the fight shortly before the boss death, trigger cutscene, where you show how boss falls on the ground and changes in cloud of dust or something similar.
But if you talk about normal common opponents dying in vast numbers...well I suppose it can be done the very same way, but without the cutscene. You will probably need to add some cloud, so the exchnage of the model wont be visible, or at least not disturbing.
Im afraid itll also require some scripting and I know nothing about that, so cant help you there.
Also this is just a theory.
Hope its better than nothing