Can a grounding conductor from equipment terminate in a metal box grounded via EMT?
Yes, it's allowable to tie a ground wire to a junction box and let the metal conduit carry it the rest of the way back. 

However, if the ground wire is already in the pipe, I'd leave it in there - belt and suspenders - unless you need the conduit fill.

You terminate a ground wire at a junction box by attaching it to a ground screw.  Virtually all junction boxes have a hole tapped #10-32 specifically for ground screws, which are sold either with or without pigtails.   You can put 1 wire on that screw, or any sensible number of ring terminals.   Make sure the ring terminals are UL listed for use in mains power.