On Megs:

Hey the guy had one arm left. I'm pretty sure it looked like a great idea.

I myself was shocked that Prime successfully pulled an ESRB-maker on Megs in the state he was in. Just shows how badass he is.

 

I think, ultimately, Sentinel wanted Optimus to live and eventually revive Cybertron together, so he let Optimus keep the matrix it, both in good faith and probably feeling some guilt over what he was going to do.

As far as Megatron, well Megatron just shot him to shoot him and it was at the right time. Optimus wasn't going to let either of the genocidal maniacs live, but for some reason a lot of internet posters don't understand why Prime would do such a thing.