Wiping the SD card using standard disk tools would not affect the SD card's firmware. SD cards are not dumb storage devices; they have built-in CPUs that handle DRM, protocol interfacing, and wear leveling, possibly among other things. That CPU has its own firmware, which might be reprogrammable by an attacker that knows the right commands to send.
Fair enough, I didn't think about that. I guess if you were using a RPi for a quarantine job like this, you would consider the SD cards as one time use devices and destroy them after use. The RPi itself shouldn't be affected though.
