To Kill or Not to Kill - Zeke in Deus Ex 3

Solution 1:

Killing him where you did actually makes it slightly easier on you later.

Without spoiling it, you'll only see him again one more time throughout the whole game and he's hostile, so you need to either kill him or knock him out anyway (without interaction). So killing him where you did just removes one more obstacle later in the game.

Solution 2:

Zeke does appear later in the game, although you don't have much of a meaningful interaction with him.

After arriving back in Detroit, you eventually need to track down Isaias Sandoval. William Taggart reveals that Zeke is his brother. When you get to Isaias's apartment, Zeke is there and you need to take him out (lethally or not is up to the player). Zeke doesn't really say anything (at least he didn't for me), but I quickly stunned him and continued on with the quest.

Solution 3:

From the Deus Ex wiki:

Zeke can also be killed after the standoff, if the player talks him into freeing the hostage; later, when he contacts Adam with information he can be killed with no negative repercussions. He can also be knocked out but there seems to be no way to get the police to arrest him. He has about 500 credits on him.

Solution 4:

I then decided to kill him and earn brownie points with the Boss, but Jensen never mentions it.

One more outcome you may wish to try is to not negotiate with Zeke, and quickly shoot him with a stun-gun. That makes SWAT and Sarif happy, because the hostage is saved and you've also apprehended the perpetrator.

Would Zeke have popped up after the first time I left Detroit if I hadn't killed him?

If still alive, he makes a hostile appearance when you return to Detroit later, but with no conversation or anything, he just acts like any other hostile Purity First guard.