Prime didn't kill anyone in the cartoon. Ever.
In fact the cartoon was pretty low on violence.
I'm now going to put too much thought and effort this...but....
The Transformers are at war and war doesn't tend to be particularly nice - so it follows that Prime would also do some not particularly nice things.
His motto has always been 'Freedom is the right of all sentient beings'. The Decepticons threaten the freedom of the humans, so it makes sense that Prime would use extreme prejudice to deal with them.
