This story has a much different feel than your usual fare of Megatron/Starscream, and that's certainly not a bad things as the dynamics between these two are very different, indeed.

How so? I'm just not sure what specifically you mean here.

perhaps his naivety in dealing with the other faction on a more person level gets the best of him in this story.

That's what SS is banking on, yes. :-)

I can certainly see Starscream's up to no good, but poor Optimus gets the wool pulled over his eyes!

Hmm... maybe I need to revise. He's meant to be aware that SS is up to no good. He just can't resist trying to help, as he sees it. To leave Starscream there and ignore his asking for help would just tear poor OP up inside. He's not agreeing because he's naive so much as because he can't refuse, and SS knows it.