It seems that screwing off to go do other stuff for too long might break her.
I can't confirm that. I'll usually do her fight at a pretty late stage in Act I - probably before Nere but well after doing the Goblin-stuff and also well after the Tiefling-party. I'm usually at or very close to level 6 when I deal with Auntie. And I've never seen her AI glitch out like that on any versions/patches of the game.
The only obvious differences between my usual approach and what you describe is that I don't kill the Gur-hunter and I don't engage the Redcaps before entering Auntie's hut or lair. Oh, and I also don't rob her place before I "kill" her. I'll just wait for her to move into the rear of her living area and then sneak through the fireplace unseen so I can avoid that pointless first fight in front of the fireplace.
I'll typically go to her relatively early to trigger the whole "eat up, Mayrina"-sequence and then trade with Auntie a couple of times if I need those STR-elixirs. So she'll be "in limbo" for me for quite a long while before I start her quest in earnest.