I don't see what the problem is with the paintball or pepperball guns.
Agents are often facing small groups of people throwing rocks. These rocks vary from large marble to fist size. They can kill people. To an agent working alone, the available options are to retreat or defend themselves. Currently, the only tool an agents has to defend themselves from any sort of distance attack is their issue sidearm or a long arm that they check out before shift.
This is not new. When I was an agent the specialized teams were already using them. I'm guessing (no first hand experience as I left over a year ago) that they worked well and are now available to other agents.
If someone has a rock in their hand and they are 10 yards away, they can hurt you. Badly. The thing is, you aren't typically allowed to shoot someone for that. You can tell them to drop the rock, but they don't have to comply. OC spray would be great for this situation, but it has a limited range. The pepper ball guns could be used in such a situation.
If the gun fails, or they start throwing rocks, it isn't hard to toss the pepper ball gun, draw, and go to lethal force.
As Biker said, it is another tool. It serves a specific role, and it has a place. Like any other tool, it is wrong to misuse it.