Just want to drop a note to say I can't think of a way good way.
As you pointed out, SYSCFG can do it, but it is not tested on debian.
Restoring the BIOS defaults via the iflash tool would set the serial port to defaults, but it would also change any other BIOS settings that were not at defaults.
you could enable SOL via IPMITOOL, but that is not the mother board serial ports
Network re-boot to WINPE or a linux verson that suports syscfg.