Just record it into WAVE format which is also lossless.
However, you should be aware, that even though the minidisc format is digital and compressed, there will still be additional loss, as recording through line-in includes having the minidisc player outputting an analouge signal to your minijack cable, which goes into your soundcard.
So basicly you're recording goes like that.
LIVE-Performance >
eventual amplification or equalisation >
Digital WAVE-synthesis generated >
ATRAC3 compression performed >
ATRAC3 decompression performed >
Eventual amplification, equalisation or add of 3D effects DSP's or similar >
Analogue signal generated and send through analouge cable >
Another Digital WAVE-synthesis generated >
Eventual amplification, equalisation or add of 3D effect DSP's or similar >
Final WAVE-file ready !
Once you've recorded it, you can always encode to FLAC or Monkeys which will generate no further loss or affection, or encode it to OGG Vorbis, MP3 or MPC which will generate additional loss.
I'm not sure if my processing-explanation is right... it just how I would picture myself if I was live audio going through a minidisc to FLAC-format.