The Scholomance's fondness for maleficers makes a certain amount of perverse sense after The Last Graduate. As El speculates, the school's only motivation is to get as many kids out alive as possible. Most kids who turn maleficer are loser seniors who don't have any better options and do so out of desperation. And who do they target? Other losers who don't have any allies to watch their backs or avenge them. So if the choice is letting one kid out at the expense of a few others who probably wouldn't survive anyway, or watching them all die in the graduation hall, what's a sentient building to do but call it a net win and move on?
Then there are the other type of maleficers, the ones like Liu who come in with a small box of mice and a plan. These ones are even better as far as the Scholomance is concerned, as they're self-sufficient when it comes to malia and don't need to target other students.
If the Scholomance wants to keep students safe, why did it so ostentatiously bribe El to let the maw-mouth alone in the first book? It didn't. It wanted her to take the maw-mouth out. She almost couldn't—she used nineteen of her twenty-seven filled crystals to do it. And she gave up a perfect chance to show off (or her belief that she wanted to show off and then have a life in an enclave) to do it—the way magic works in this universe, that sacrifice probably gave her a significant mana boost and might well be the reason she could kill the maw-mouth at all.
When El was trying to join Orion in the main library, the shelves stretched on and on; when she turned around and saw the maw-mouth, she had no trouble catching up to it. Seems pretty clear where the school was directing her, despite how El interpreted it.
The idea is reinforced in the third book after it reveals El was born with so much power so she could be in place to kill the half-maw-mouth Orion before he could destroy the world. The school knew her destiny was almost here and was beginning to prepare her for it, showing her she could kill a maw-mouth and then go from there.
