Nick didn't want him to, he really didn't fucking want him to. He heaved a sigh and gave the order, "Stand down, I repeat, stand down. Iron Man is not a hostile." A lie, sure, but Fury figured that even in all his, well, fury, Tony wasn't going to take out a helicarrier full of relatively innocent people just to kick Nick's ass. Or try to, anyway. Nick could take a motherfucker on. Hopefully it didn't come to that, he did have the very reason Tony was here, after all (he really should've been expecting this) and he could use her against Stark if he had to.
On the deck the guns all stood down and stepped aside to allow Iron Man into the bridge. Couldn't be too careful, not when there were zombie mutants around or assholes in armor with a grudge. Nick waited at his command center, feet splayed and arms behind his back. Best to get this done with quick.