Whereas in case of the first game the Amiga version was at least superior in terms of audio I think there's no reason to prefer the Amiga version over the DOS version in case of CF2. IIRC they included all the audio from the Amiga version this time (including the theme song with vocals and all ambient sounds) and only in the DOS version you will get graves as you loose soldiers - the developers skipped this feature for the Amiga version due to memory issues.

Arguably there's some slight balance issues, some claim that the Amiga version is harder, others that it's the DOS version but I really can't say that either version is superior gameplay-wise. So you can play the DOS version with a clear conscience.

Edit: I have to make a correction. While they *did* include the music from the Amiga version in case of CF2 (including the vocals) the in-game audio is still worse. Apparently it's again missing most of the ambient sounds and they reused the gun sound from the original game instead of using the new one made for the Amiga version of CF2. Sorry for the wrong information before. For some reason I was perfectly sure that the ambient sounds were present in the PC version of CF2.

Oh yeah, another weird thing about the PC version of CF1: for some weird reason only the squad leader receives kills even if one of the other guys delivers the shot that kills an enemy - the only exception is when you split your guys into several teams.