I think keeping the 8U2 in reset is the simplest option, and there shouldn't be any issues involved.
You could also update the 8U2's firmware to automatically "get off" the serial lines when the bootloading process is complete. That takes a bit of coding but is a nicer long-term solution as it requires no manual intervention.
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The Ruggeduino: compatible with Arduino UNO, 24V operation, all I/O's fused and protected