If you're Immune System turned against to what would you do?
You can't do anything by your own power. It's inside you. It's what's supposed to protect you from threats like this. So, what do you do?
See a doctor, get prescribed and take medication.
The pills you take go in your body and fight the virus for you. You can't do anything, but hope they win.
In the same way, Mata Nui was made with pre-prescriptions. The Great Beings thought of everything.
When Mata Nui faced a problem he would use the tools the Great Beings made him. *notable tool where the Toa who came in Toa canisters.
Mata Nui wasn't meant to do anything, besides leave, learn, come home and restore Spherus Magna. The Toa and the Brotherhood of Makuta would take care of his body for him.
Like I said whoever gave anyone their personality inside Mata Nui is at fault, not Mata Nui.
Mata Nui was not a god or religious figure. He was just a really powerful robot.
Mata Nui was not a leader either. (He had to learn to become a leader on Bara Magna.)
Mata Nui was a somewhat simple robot who had a very simple purpose.
And true, if Makuta never gained his personality no one would have died or gone through so much turmoil
But, we also never would have met Tahu or seen the island of Mata Nui.
We never would have seen the Mask of Light or Life.
The Matoran would have been mindless robots with only the purpose the master gave them. They would never had been free.
If none of this ever happened,
Mata Nui would never no what good is. He would live, complete his duty and die.
So Mata Nui wasn't a jerk, he was mindless. But, now through what's happened he can live and choose to do what he wants for once, he's free!
In the end Mata Nui let the Toa and Glatorian choose their fate. He will not interfere because he understands that he is not fit to be their leader. And, he chose that willingly.