It seems the producers did handle it well in terms of working with Zeke:

"We started having conversations all the way back in Fiji nine months ago about the care with which this episode was going to be handled," he said. "I came to Jeff [Probst] and asked if I could write a personal essay about what happened and he immediately said yes."

In a statement provided to CNN, CBS stood by its decision to air the outing.
"After the tribal council scene in [Wednesday night's] 'Survivor' was filmed, we consulted with Zeke Smith and with GLAAD in advance of the broadcast, including the issue of how Zeke would tell his story after the episode aired," the statement said.