There is no software against the hack available right now. So basically you can't protect yourself against this hack. Some people claim that you'll know when a player cheats if you are an experienced War2 player. Of course if you are attacked by flying juggs or exploding peasants everyone can tell that the enemy is cheating. The problem are the subtle cheater that use the hacks to get a few extra units (in crucial phases like the startup and after attacks). It will be next to impossible to tell whether the other player is cheating or not.
This problem will mainly hit good players. Some people still don't know about the lumber bug or how to start; for them, a normal (good) startup looks like magic anyway. People will always despise each other when losing, because you will never know whether the other one was using unfair means. This is probably the most destructive aspects from hacks for the affected games. Shlonglor is right, until there is a solution, War2 will not be as it was before.
What to do in the meantime
I hope that a patch against the hack will be released soon. My idea how to stop it should be easy to program, but it is not perfect enough to stop future versions. Sigh... Blizzard should be aware of the importance of that special case; for the first time, a hacker wants to see money for his work! So there are still economic interests behind writing a patch. May they be stronger than schedule and budget problems! If Blizzard does not act against the hack, this will encourage people to hack up future games, and may be ruin the software industry in the long term.