E&M over microwave or T-1 channels works quite well for our 6 meter repeater here in Indy. We use an older N9EE controller with relay isolated PTT outputs. You will probably want to isolate the controller from the E&M with something. Most E&M systems require either -24 or -48 VDC for keying. Our system is all GE MASTR II with 5 voted receivers coming into a central site where the voter is. The output of the voter goes into the controller which keys the M lead on a microwave channel to the transmitter at a site about 4 miles away. At the transmitter, the channel's E lead keys the transmitter PTT input. It works out quite well. Hope this helps.
Mike, WA9FDO IPL-ARC