Right now, I don't see Petyr as feeling even remotely threatened by Sansa - and whilst I'm not discounting it, I don't see Petyr as leading up to an elaborate and ironic vengeance upon her either. Sure, he'd push her out the window himself if he needed to, but how much more satisfying to bring her to feel (some sort of) love and trust in him, educate her just enough to hold her own (whilst still bringing all her knowledge to him for advice) and then place her in a position of moderate power, knowing he can rely on her to protect him and further his interests?
Classic grooming process. Right now, I'd also say it's in her best interests to go along with it. He's a helluva player and she'd be wise to keep him on her side.
Petyr also had Lysa poison Jon Aryn (a dear friend of her father's), and had a hand in Ned's downfall as well. Sansa heard Lysa say as much right before she was shoved out the moondoor. At some point Sansa will put 2 + 2 together and play the game without Petyr.