um, watch the animated 86 movie.
"You, who are without mercy, no beg for it? I tought you were made of sterner stuff, Megatron."
says Prime just as he's about to shoot the battered Megatron who's ass he just whupped. is that so different to Bay Prime who executes Demolishor and kills The Fallen?
Yep. And also read some of the G1 and G2 comic books where war was brutal. Robots got wrecked and torn up left and right. The 80's series was a product of its time and frankly couldn't show characters getting killed left and right for a variety of reasons. The 86 movie released them from those constraints (while also being a tool to pave the way for all new toys). The way this movie portrayed the war is consistent with several past portrayals, and the way I'd expect a war between two factions lasting millions of years to be.