They would be cautious and capture him to find out who/what he is, and if he has anything to do with the case they’re on. He’ll probably spend some time under a vase (at Dean’s insistence), while also getting to eat the pizza Sam offers him.
If Dean leaves the room, Sam will take that moment to give Jacob some air, letting him out of the vase. He’s four inches tall, no wings, and they have his climbing supplies, what’s the worst that could happen?
Being small around one giant Winchester can be nervewracking enough, but both of them? They’re such strong personalities compared to Jacob’s very relaxed nature. He’d be so cautious with everything, and also probably surprised they could catch him so fast. Those guys are speedy!
With Dean out of the room, his intensity is gone, but there’s still a curious Sam to deal with. I can see Jacob trying to sidle away when he thinks Sam’s not paying attention only to be dragged back, maybe poked for his trouble.
Brothers Apart 