I believe what the OP wants is to still sync the dock but without messing with the icon size.
If I am correct, there is no setting for this. the dock sync is a on/off option only.
That said, you can try the following, which I have not tested ...
In the terminal you can the icon size you want on each machine by typing:
defaults write com.apple.Dock tilesize -integer 48
change the 48 to the size you want.
Then lock the dock size by typing:
defaults write com.apple.Dock size-immutable -bool true
This prevents the dock from being resize using either the "road" divider on the dock or the dock settings window. It "should" prevent MobileMe from changing the size as well, while still updating the dock items on both machine.