For all his reservations about interfacing, it seems he's very certain of one thing, now that the option is presented to him. Yes, Aperture is where he belongs, and it's very nice of Samus to even offer, but even the question has him shaking his inner component in a "no". It's an impression imitation of a human gesture, all things considered.

"Oh, no. We can't go back there. She'll kill us."

The us is pointed, like he's entirely certain that GLaDOS would not discriminate between Wheatley and anyone who happened to accompany him back to Aperture.

"Besides, I'm not even--I don't think I'd know how to get back, at this point. Looks like I'm, uh. Along for the ride. For the time being."