How can I disable the iPhone's microphone?
If security is a major concern, I'd assume that a software hack is not the solution. There still is a chance of malicious software importing code which re-enables the audio functionality. 

I read NSA guidelines for Mac OS X 10.6 about disabling iSight on Macs where is was recommened to physically remove the webcam for absolute security.

If you do not want to physically remove your iPhone's microphone, I would try to distort the audio as good as possible - that would leave a spy with imprecise mumbling noises. The iPhone 4 can be muted quite effectively by just closing the hole at the bottom. There is a good chance that closing the hole of the microphone has the same effect. You could apply prestik or hot glue for example.