Cuttermaran is a cut program for MPEG1 or MPEG2 video streams. The streams can be cut without recalculation. The asynchronous between audio and video will be minimized.
Cuttermaran supports frame accurat editing, but you will need TMPGEnc 2.5 for smart rendering. There are available a few freeware encoders, too. Take a look at the provider section.