Well, I decided to answer my own question. Went to the Prophet, killed her and got that nice 45 flame resist amulet. Went back to the Undermother and got the option to attack her.
Goddamn is she strong in her unweakened form, David really did mean for her to be impossible. After dying a bunch of times I just decided to cheese her with Jack's suggestion - I went back to town, grabbed some random shitty bow and a speed potion, cleared the cave of the small cannon-fodder Mirmeks and initiated battle with the Undermother. As soon as it started I popped my speed potion and ran into the big room with the stalagmites in the middle, then ran around them until, eventually, her fat ass got stuck. What followed was a long 10-15 minutes of me, a 2h warrior, popping arrows into her hitting for constant 2s, occasionally critting a 3, but at last her healing stopped (she seems to have enough mana for three heals only) and she went down like a sack of potatoes.
Might not have been the most honourable way to deal with an ancient creature, but she's a nasty bug and I really wanted that hide.