Coulson also kept him around to keep him in check when he was Director.

He's not bigoted.
He's pragmatic and the sound voice of reason. He's the one who's going to give caution when everyone else wants to jump right in and try it.
He's distrustful of alien and weird tech. It's the reason that Coulson put him in charge of anything acquired of that nature.
Coulson knew that Mack would not be tempted to use it and would make doubly sure that it was kept out of the wrong hands.

I still hate the Mac character, because he's just unnecessarily cautious and pretty bigoted, BUT, the writing for his character has definitely improved, and even though I still dislike him, he's a character that is well developed so he's a "love to hate" kind of character.
I feel like they may be setting him up for a death scene or betrayal or something because he seems really, really unlikable atm