I know what you're after, but since FLAC is lossless, there isn't really much to be gained from editing it in its compressed form - uncompressing a FLAC to a WAV, editing the WAV, and then compressing back to FLAC will not change the sound quality at all, while the same operation with MP3 or OGG would very likely introduce additional artifacts due to lossy recompression. I guess if you had a huge FLAC file - a few hours in length, for instance - it would save disk space during the editing process, but that's about the only advantage I can think of.
The closest I've found to a native FLAC editor is
CD Wave Editor. It's shareware, but it does have a 30 day trial period. It still doesn't edit FLAC natively - it does exactly what I described above, but internally.