He lets Jon go only because he gets the feeling that even fighting back won't change things. And when he does, that is when he notices the eyes. Okay. Well. That's happening then. Sam's eyes go from Coraline to Jon then back to the pockets of chaos around them, feeling the time tick down.

"I'll go get him." He says it like he's decided it, but then turns his attention back to them both. "You two go to the portals and wait for him there. I'll go find him and send him your way. But only-" Sam looks pointedly at Jon, and then Coraline. "If you two make it through in time. I know you know, or whatever, but I'm serious. Wait for Martin but then get through the portal. Okay?"

They aren't orders, necessarily, but if there's a little Captain America woven in there, Sam can't really help it.