You should never design any circuit so you have a "high" signal going in to a powered-off device, unless it's using some form of interface specifically intended to handle that situation, like RS232, CAN or RS485
Use open-collector (active low) for basic logic signals, so the only "high" level is generated in the target device.
Just use schottky diodes to emulate open-collector, with pullup resistors on the target inputs.
For the serial input, just connect a fairly high value resistor between the USB adapter and MCU pin. That should have no effect on the data but limit the possible current feed.
(That's also a kludge way of limiting interaction between the powered and unpowered boards).