Its a gameplay decision because fighting a horde of mostly jackals would get very dull after a while - grunts are simple to defeat and play a comedic role with their dialogue. Having grunts on the player side may have also caused confusion (from the developer's perspective; i personally think it wouldve been fine) which is something bungie wanted to avoid which is why elites have the ugly green phantoms in h3 (so they are not confused with the regular phantoms)
Lorewise i think its some grunts sided with the elites and some went along with the brutes. They basically went along with whoever was commanding them.
Youll note that the same thing happened to hunters between h2 and h3