However I'm totally new to SCSI and all the horror sories about termination and different SCSI standards make me nervous.
Don't let this scare you, as it is in fact pretty simply. Termination can most times be fixed with a simple jumper, other times with a dongle to connect to the cable. SCSI standards aren't difficult either. You can get 50, 68 and 80 pins drives, but all can have adaptors attached so they can go to the needed interface.
As for the MK2 SCSI module; it uses 50 pins drives, so this would be the easiest thing to look for. You can get a 68 pin drive though, and buy the needed adaptor for it, as the 68 pins will most likely give you a bit more performance.
SCSI is a more expensive option, but for most people the money is well spend.
Going to install a new hdd on my own CSMK2 SCSI controller this weekend :-)