Now that I've played a little bit, binding directly to the alt or control key isn't that bad. BUT there needs to be consistency. It appears that when in working on the workbench or in a furnace, the key binding defaults back to a 3 button mouse... and not what the key binds are set to by the user.
IF there was consistency then I believe users could get used to this. Otherwise, it feels like the bindings only apply to certain parts of the game.
I too am experiencing the missing ctrl-click and option-click on the Mac (specifically the MacBook Pro)
I for one believe it is fixed.
The perceived problem may in fact lie in the difficulty in setting the key bindings back to button 2/3.
Maybe a 'set to defaults' button could solve this?
I had to edit the options.txt file located at: (specific to a Mac ONLY)
/Users/[username]/Library/Application\ Support/minecraft/options.txt
and set the following items near the bottom of the file:
key_key.attack:-100
key_key.use:-99
key_key.pickItem:-98
Once this was done, and the app restarted then all was as it originally was.
IMHO, The 'sticking issue' should be moved to another ticket.