Stark and his fellow humans have proven to be extremely persistent pests to not only Thanos, but multiple versions of Thanos. Squishing the bug now is the safe thing to do. The *satisfying* thing to do. But it isn't the *smart* thing to do.

He releases Tony's head. He doesn't take Tony's hand, though.

"You've been here for some time," Thanos observed. "And you aren't alone."

Stark was desperate, and only questionably useful. But he had intelligence. And he was right, there were new enemies now.