I think in his mind, school was how hell get job and finally have some control over his life. Hes still very young so in his mind; that was the only way hell stop being dependent. So it makes sense, hes not thinking clearly. Losing this one opportunity is like hes whole world shattering. Also; we dont know if omega farmers exist or if omegas had a safe life in the countryside and running away. I mean there was thag chapter where they watched a live show of omegas hunted and attvaked by wolves. Finally, this btvh ML having too much power.
Not EVERY one has escaped from the toxic ML. Also, I think you're forgetting an important key item that the MC has right now.... Remember that necklace? The one he can't remove? Well. That's a leash binding him to the ML as well. Of course, you have free will to choose to continue reading or not, like I did with Barge In. Now that was toxic af.

Boy, you gonna sleep with him to go to school? Sleep with him to get a job? Suffer all that abuse for what? Better run off the country side and work as farmer because the future that awaits you is HELL!