Yes. Audiograbber already supports FLAC as external encoder.
1) Just get the official FLAC for windows here (with installer or just the command line tools - you just need flac.exe):
2) Go to "MP3 settings" (it is named "mp3", but it works for any format), "external encoder" and browse for "flac.exe".
3) Use it with the following command line:
[<general-options>] [<format-options>] [<encoding options>] %s %d
(the %s %d is the param Audiograbber uses for input and output file)