If Thanos is so evil, why did he destroy the Infinity Stones in Endgame?

Thanos (in infinity war) isn’t evil.

He’s worse.

He’s a self-righteous zealot, the most dangerous kind of villain.

Thanos isn’t interested in personal gain, personal aggrandisement or even pure power.

He isn’t chaotic like the Joker, looking to cause discord and anarchy. He isn’t vengeful or vindictive like Killmonger or The Vulture. He isn’t selfish.

He doesn’t exhibit the seven deadly sins:

• He isn’t consumed by lust- we don’t see him commit any sort of amorous transgression
  He isn’t greedy - we don’t see him attempt to use the stones to amass more wealth or power
  He isn’t gluttonous - we never see him overindulge in any pleasure
• He isn’t slothful- he doesn’t delegate tasks unnecessarily, and he tirelessly works towards his goal
• He isn’t consumed by wrath- hardly anyone in IW is able to anger him (unlike his younger self in endgame). Even when Iron Man makes him bleed, he only loses his temper briefly
• He doesn’t envy anyone
• He isn’t prideful- hardly ever gloating or puffing himself up above others, even his underlings.

Basically, Thanos in Infinity War is a kind of religious Zealot. He has given himself over completely to the doctrine of achieving balance through mass slaughter, and he has a single minded vision of a grateful universe flourishing after he wipes out half of its population.
He is so convinced of how correct he is that he believes anyone who has a different opinion is just misguided- which is why he hardly ever kills anyone he doesn’t need to, instead treating them like stubborn children.

A zealot cannot be reasoned with, bargained with, and cannot be motivated to stop, as they are even happy to die themselves in the service of their goal.

They are motivated entirely by ideology.

Thanos isn’t motivated by logic. If he was, it would be clear to him that

1. Balance doesn’t mean you empty half of the scale: that throws everything OUT of balance, as we saw in the young Gamora scene
2. Doubling resources gives the same effect as halving population
3. A halved population will repopulate even faster
4. An all-powerful infinity gauntlet can solve the problem faster by reducing consumption needs across the board

No, he was motivated by a doctrine of mass slaughter in the form of a total dogma, immutable, unchangeable, pure ideology.

And in this case, Thanos’ ideology told him that nothing must undo what he has done.

The stones had to go.

So, devoid of earthly desires, greed, lust, or even care for his own safety, he did what his ideology demanded he do- and wiped out the stones.

Then he retired to a simple life with very few real pleasures, and didn’t even put up a fight when his life was threatened.