“If quirrel can get a troll into Hogwarts...”
It was not Quirrel, but Dumbledore, who got troll into Hogwards. In analogy to canon, Dumbledore brought a troll to Hogwards as a training device for Harry and Hermione, see the book HP and Philosophers stone. In canon the purpose was fulfilled, because the children had some sparring with troll and defeated him safely afterwards. In HPMOR, the plot is reversed, because neither Harry nor Hermione fall for this training trap. When told they should NOT go to Hogwards basement, because the troll is there, they are immune to the reversed psychology. Rather, they reasonably decide to obey and not to do the dangerous thing. They simply ignore the basement. Dumbledore makes another try later by telling Harry once more NOT to go to the basement and NOT to use the Alohomora spell to unlock the basement door. In vain again. So the troll stays in the basement for a long time, until Quirrel unleashes him, transforms him to be sunlight-immune and uses him as a weapon on Hermione.
OK, I admit, maybe I do not remember canon as well as I thought. I am sure, Dumbledore made some RPG game there for Harry and company, Hermione had a mathematical puzzle there etc. Was the troll plot separate from that RPG ?