Of course, the fact that the original script had more violent undertones led to some urban legends that there exists a cut of the movie with such scenes, or one where Prime's body crumbles into dust. But AFAIK, they're just that - amusing legends.Magnus was supposed to have a more elaborate death scene on Junkion, and a brief part of it was left in. He was to be drawn and quartered by the Sweeps, but this was decided to be too graphic. If you watch when they open fire on him, their beams are still solid. Shockwave's death was also referenced, but not mentioned directly in the movie.
The drawing & quartering appeared in the comic adaptation of the movie (I should know; I read it a zillion times before finally getting to see the movie!)
There are always rumours of other violent deaths as well. I definitely heard somewhere that the reason that Prime appears to awkwardly stand up from a crouched position as he challenges Megatron one on one is because he'd just finished off a Conehead (I forget which one) in a particularly savage battle. I don't think there's any truth in it though.
http://www.wombatking.com/coppermine/thumbnails.php?album=4&page=3
The storyboards on this page show Prime fighting triple changers before Megatron - losing his gun and fighting Blitzwing hand to hand, so I guess that's the missing scene.
Fantastic link! Thank you!