Yes, the panel is a 120Hz panel, so no matter what, the picture will be upconverted to 120hz.
The AutoMotion Plus is picture processing that takes the upconverted signal and processes it further. Turning this feature off doesn't defeat any 120Hz picture at all.
Does that help explain how that feature works?
I just bought a Samsung LN40C610 TV (40" 1080p 120hz auto motion plus), and I was wondering, if i turn the Auto Motion Plus feature off on this screen, does it still display images at 120hz?