There's a big difference between not fearing a building blowing up and realizing that a bunch of Sith apprentices could gang up and kill you. It's quite simple, with an army the Jedi would become aware of the Sith and would start hunting them down which they did a thousand years before TPM. But with only two they can stay in the shadows and infiltrate the Republic thus destroying it from the inside. They can catch the Jedi in the perfect trap. When the Sith were numerous they failed but when they were only two they succeeded so I don't see how it can be called a bad idea.