Having SIGNIFICANT experience with both of these subjects, i think I should be able to help....I have 2 Sony MD recorders, and both sound wonderful....(for those of you wondering, yes the MD uses compression, but it is so finely developed that the sound quality is still very good...in fact, only about 10% in this BBS could tell the difference)...however, MD is not very widespread, and many people won't be able to listen to it....
so on to CD....the only problem you're facing here is the quality of the converters on your sound card, and the quality of the hard drive you are recording on....if you're using a regular consumer PC (compaq, dell, etc.) chances are the hard drive will be an IDE format and relatively slow...also, if you only have one drive, it is being constantly accessed by the system, slowing it down (there is a common myth that digital is digital, but there is a certain amount of error allowed in the recording that will adverse artifacts)...as I said the converters on the sound card also play a HUGE role...chances are the converters on the MD will be of higher quality than the sound card, and also free from the computers internal noise and intereference....if your sound card has a digital in, you may be able to buy an inexpensive converter such as MidiMan's flying calf A/D....
Personally, if I were you, knowing what your current setup is, I would stay away from using the computer and buy a NON-PORTABLE MD such as one of the lowend Sony's, which run for about 200-300 dollars...