Are the grunts and hunters in Halo 3 your allies

Sadly no, the creators of Halo 3 felt that if you had hunters and grunts as allies(the ones that sided with the Elites) and enemies(the ones that sided with the Prophets and Brutes) it would confuse the player.

But some still stayed sided with the Elites, but you just don't see them in Halo 3, you see them in Halo 2 during the Covenant Civil War.