Should I avoid ground loops in branch circuits through conduit?
The "ground loop" in question does not matter one bit -- the NEC assumes all involved EGCs are connected together at all junctions, even.  (It's impossible not to have them all connected together in a metallic conduit system, for one.)

Note that there are a few exceptions for isolated grounds for certain sensitive equipment, but the benefits of isolated receptacle EGCs are unclear. (Note that the redundant earthing requirement in patient care areas is not an isolated equipment grounding requirement!)