Theoretically, the best way to take care of them is to have the UN increase economic sanctions on the Iranian "Government", basically crushing their government, and forcing a regime change as peacefully as possible. Since that is out of the realm of possibility, because the UN doesn't really exists, we have to hope we can avoid an all out war.
I do expect the worst, which means an all out war with Iran, and you always hope to avoid civilian casualties, but they are always an inevitability in war. I thin a war with Iran would be much tougher and the death tolls would be far higher than with Iraq- but to let Iran continue on their current path in suicidal