NEC code regarding grounding and conductor pass through
Don't mix up your EGCs and your GECs!

The EMT, provided it is made up properly and is not excessively exposed to physical damage, is a perfectly fine ground (equipment grounding conductor) by itself in this application -- 440.9 in the 2017 NEC only applies to runs on roofs, which get tread on repeatedly by clueless folks:


  440.9 Grounding and Bonding. Where metal raceway is run exposed on a roof for air-conditioning and refrigeration equipment, an equipment grounding conductor of the wire type must be installed within the outdoor portions of metal raceways using non-threaded fittings.


However, the ground rod needs to go, because it inadvertently violates 250.121 by trying to use the EMT as a grounding electrode conductor that ties a remote ground rod back to the main panel bond atop it serving as an equipment grounding conductor:


  250.121 Use of Equipment Grounding Conductors. An
  equipment grounding conductor shall not be used as a
  grounding electrode conductor.
  
  Exception: A wire-type equipment grounding conductor installed in compliance with 250.6(A) and the applicable requirements for both the equipment grounding conductor 
  and the grounding electrode conductor in Parts II, III, and
  VI of this article shall be permitted to serve as both an
  equipment grounding conductor and a grounding electrode
  conductor.


So, just rip out the errant remote ground rod and whatever wire was hooking it up to the disconnect(s) or just the wire for that matter as the errant rod will do nothing if it isn't connected to anything, and all will be well when the electrical inspector comes around.