We have an outcome pump on our hands that says that Harry is going to tear apart the stars. He can do that for better or worse reasons, and with a better or worse outcome. Quirrel thinks that a Harry that isn’t crippled by a centaur (since Quirrel already knows Harry won’t die) has a better chance of producing a good outcome than another Harry.
Remember that he offered in chapter 95 to read some of his science books and speaking of what comes to mind (...about a month ago. Why isn’t Harry omnipotent yet? When I read that Quirrel’s suggestion, I thought the rest of the story would have to be squeezed in the time it takes Quirrel to regain sentience.)
It seems plausible that Quirrel read the science books and isn’t going to tell Harry anything reality-breaking, since he did a similar thing with the library—after telling Harry that Memory Charms are just filed under M, he says he’s going to put some of his own special wards on the restricted section.
It could always be possible that Quirrel’s “special wards” happen to let Harry through more easily, or allow Harry to browse the section more covertly, though I’d put odds of that fairly low given his mention of the situation to Minerva.
While I didn’t realize Quirrel might be lying about his willingness to cooperate, the Memory books aren’t in the restricted section and we haven’t heard anything about him sabotaging Harry’s attempts at taking over the universe since chapter 95 (except for some sort of deception in 100⁄101… “what a fiasco” is not something you would hear Quirrel say to himself audibly and honestly). Maybe he was in Zombie mode until 99? We wouldn’t know, since we weren’t in Harry’s POV since 2 days after that chapter, although in his shoes I would have attempted contacting Quirrel as soon as possible.
While both the former and the latter are entirely plausible things for Quirrell to do, it is also worth noting that Quirrell would happily play the Role of a concerned tutor before McGonagall at this time. It would make her trust him more at a time when he may need to use her and other teachers on short notice to fulfil his own objectives, even if he doesn’t intend to do anything about the Restricted Session at all.