I've installed two MSD's that way on two seperate ('78 and an '83, both small blocks) dodge trucks. The owners have never conveyed any problems to me.
Here is what I *think* happens, since only one of the two wires has power at a time. Yes, the 'start' wire will back-feed the "run" wire during cranking (and visa-versa), but the backfeeding stops at the ignition switch. Why? Because if there is no contact being made to provide the 'dead' wire with power, then there is nowhere for power that is back-feeding to go past the ignition switch.
That is how it seems to work in my mind. If I am way off base someone please correct me. But I have had no problems with simply connecting the wires.
'73 - Your options are to (1) remove the ECU, ballast resistor, and the associated wiring no longer being used, or (2) leave everything in place, with the wiring tucked into an existing harness or new loom, with the 'dangling' connections insulated. If you plan things out ahead of time, you can use connectors that will allow you to easily hook up the original ignition in a bind.
-S/6