As FutaFred said, it is not at all hard to avoid this. Just do the following:
1) Avoid adding more than 3 new students in a week.
2) Assign new students to your classroom for their entire first week. Sorting the students by "grades" when assigning will make the new students the very last ones on the list. (Hopefully someday we get a QoL improvement that lets us flip the sorting between ascending and descending order.)
3) Advanced Physics if you have it, physics if you don't, as the initial homework until the grade situation is good.
4) Give hints during the test the first 3 or 4 days, and your goal is 15 affection for each new student ASAP, to open up home visits.
5) On home visits, the first week or so, up int 4+ times.
And beyond that, with extra classrooms and teachers, assign there based on grades. Use Social Studios as the default homework when not after something specific. And with 2 rule breaks, you can convince a mother to retract her warning. I rarely have to do that, though, as the only warnings I get are due to the Slut homework training on girls whose mothers want 100 grades... the -grades on that homework is problematic with that 100 expectation. Could be avoided with some micromanaging, but I can't be bothered
Now, you could still say that the hint giving isn't very compelling gameplay, and that therefore it still negatively impacts the game. That's a fair criticism. Though I would say that's something that would arise in part from the old "players will optimize the fun out of the game" situation. You could add only 1 or 2 new students per week, and thereby get to spend a decent amount of time doing some non-hinting each exam.
