For your specific instance, it makes sense to me to just disable the Compare plugin. However, if there are future users out here who find topic: if you still want to have the Compare plugin, but just don’t want it on the Alt+S shortcut, because of the slippery finger from Alt+Shift+S to Alt+CapsLock+S, I would recommend just removing or editing that shortcut: Settings > Shortcut Mapper > Plugin Commands > Compare to last save (Alt+S) > Modify: either pull down to “None” or to whatever key you do want for the Compare feature, then OK.
(Personally, I like the Trim Trailing and Save so much – I’ve never had reason yet for maintaining trailing whitespace in the files I edit – that I swapped the shortcuts so that Save is Alt+Shift+S and TT+S is Ctrl+S; that’s probably why I’ve never slipped from the Shift to the CapsLock during a TT+S)
