The best counter for beam spamming is to relentlessly kill the spammer til he leaves the server. You might die a few times getting close while he right-clicks a beam and blows himself up, but generally a decent player should have no problem with burying a beam spammer.
In 1.1 if a guy was spamming beams, I would make it my goal to kill only him-- and he usually just left the server or told me to leave him alone after several deaths, and he wouldn't beam me again. Even better, we used to gang bang the beam spammers when I would have a few clan mates playing with me. This is full proof, because he can't possibly kill 2+ people if everyone comes in from different directions. Just pound him into the terrain and don't let him get up. When he respawns, get back on his ass and don't let him get away to charge another beam.
You see, there's a solution to everything. Hostiling the spammer is the best way to get him to not spam you if you kill him quick and often. I'd like someone else to come up with a better solution to end teh spammage D: