Use explosives such as grenades and missiles. They'll hit Mole Rats that are digging or are already dug into the ground. If you invest in some anti-explosive armor mods like a Dense add-on, you can even drop a mine or two on yourself to counter any of them emerging below you nearby.

Berry Mentats can make it a lot easier to tell where they're hiding, both before battle and after they've seen you.

Also, you might try wearing Power Armor. It won't prevent the disease entirely but will reduce the chances of you suffering from it if you're struck (once).

Besides the tip others have given about NOT having any allies with you, including the robots.. though that bug IS fixed with the unofficial patch.. I hope this helps!