I don't know why DHS doesn't have a security team or something that's sole purpose is to protect other agents and just drop into an area and start chasing/arresting the rock throwers/harassers. They don't have to be everywhere all at once, but even the chance of a team like that dropping into a place with overwhelming numbers where people are harassing agents, and just arresting everyone who's assaulting them (legal definition), seems like it would be effective.
This might be the whole 4D chess cope, but I've considered that maybe they aren't doing this because they're letting the protestors get too cocky/go too far and then they can black bag them with more serious charges. So the inverse of this idea but in the background. This doesn't seem to be happening on a significant scale.
