Depending one what you plan to do with the pin, you may not need to do anything other than use the pin. If you are using it as input, and don't mind the pin "flashing" harmlessly during uploading or when you are using Serial statements, just use the pin. A resistor would keep it from contending with an input. Perhaps you could re-arrange your pin usage so the RXLED or TXLED pin is used for something that would not conflict with the flashing, such as input from a button.
If you want it completely free of influence from the bootloader or from Serial usage, then you will need to custom compile a Caterina bootloader that does not use that pin, or that uses a different pin, and you will need to build a custom core that does not use that pin when Serial is used. If you sketch does not use Serial at all, then you don't need to worry about customizing the core.
How many pins are you actually using? Are you already using all of D0-D13 and A0-A5? D0 and D1 are available and would only conflict if you are using Serial1. D14, D15, and D16 are ICSP or SPI pins, so those may be available, too. I was not sure from reading your post if you have already considered those extra pins.