Just sharing my own experience here. After realizing that hits to companions and allies infect you**, I went in on my own, and had a hell of a time keeping the little buggers off me. After a failed attempt to plant a mine at one spot and watching it blow up in my face immediately, I realized the mole rats don't exactly spawn in when you get close, they are there already, just under the surface and not actively hostile until they detect you.
I happened to have a rifle with the explosive effect, so the next run through, I just peppered every pile of dirt with a few shots. It worked like a charm, killing most of them before they could finish bursting out of the ground. If you don't have a weapon with that effect, it should still work if you have enough explosives to lob around. Turned an extremely frustrating quest into a walk.
** (Side note: really, Bethesda? That's some extra sharp cheddar right there.)