I use the Sony Vegas video editing software (home version) it is very simple to take a video and replace the audio track. Synchronising audio to video is not that hard. you can nudge things one frame at a time if necessary.

I'm sure this will be the case with other video editing software.

If your situation allows you to record the audio separately direct off a desk (to one of those little two-track digital recorders perhaps?) I'd go for this every time.