I've never had a problem with that. I did hear about a setup that a guy built using a time delay relay because he was concerned with that issue. I've also seen people use a diode to connect the two circuits but I've never used that method myself.
I tied the ign 1 and 2 together and never had an issue, that is a common thing when upgrading the ignition to a HEI or MDS box. I have never heard of anyone adding a diode.
The simple way to get full voltage to the ecu is to use the Ign 1 and Ign 2 wires tied together as the trigger for a relay that has a power feed back to the battery.
