I haven't played MM6 for a while, because the old computer that I used to play the game on gave up the ghost last year, and I've not downloaded the Win10-compatible versions from GOG yet.
But I think a slight change of technique would help. Try getting the bow skill for your party and arming it with bows as quickly as you can. Then, as your enemies attack, hold down the "A" key while backing away. You'll kill a fair number of monsters before they get close enough to infect your party. It won't prevent the problem but it should greatly reduce its severity. If you tackle everything in melée, your party will get diseased practically every time it's in combat.