If I understand correctly, you hit the frame with the mallet while everything was off of the bike. If this is correct then the noise is likely things like rust and debris inside the frame. If this is the case, whether it is a problem depends on your BB. If your BB is a sealed cartridge then I don't think it is possible for your debris to cause any real problem. If, however, you have the older cup and cone BB then the debris can easily get in the spindle and bearings and cause lots of wear. It will probably ride fine for a while, but eventual bearing races will wear and you end up with more friction. In this case, you will need to take the BB back out and try to clean out any debris.

One other possibility: you didn't mention when the rainstick noise is being made. If it is making this type of noise with pedal revolution, the problem is likely dirt or debris already in the bearings, or maybe no grease or something. In this case, clean and rebuild the bearings or replace BB.

Either way, its not like the cranks are going to fall off, it will just be annoying to your ears and less efficient. Eventually however, there will be more problems.