We want to protect an insulated #6 THHN with 1/2" EMT instead of PVC. Will running an insulated ground wire through EMT choke the current if it does return on that wire? I know if it is bare, EMT should not be used.

If this is a grounding electrode conductor, it must be bonded to the EMT at both ends. See 250.92(A)(3)

If this is an equipment ground, generally speaking, it has no business being run outside of the raceway or cable that contain the circuit conductors.

Thanks Tom,
The insulated #6 is for a jumper that will go from a satellite dish grounding conductor to the building electrode. To tie the two grounds together for article 810.21(J) Its one of those ground items that does not come up very often, but we want to do it to code.