I've had no problems recording direct amiga audio in this fashion previously. Just make sure you use a line-level input and not the mic-level one. With modern stuff you aren't likely to damage anything by doing the latter, but the sound will be clipped and distorted beyond recognition.
When in doubt, start off with your line-in selected as your audio source on the PC and have the recording level set to minimum, then increase it until you get to the loudest non-clipping level you can. Note that the recording level is often separate (at least on windows and most linux distros) from the normal line-in "monitor" level. The latter is what volume to mix the live line-in audio with the overall output, not which level to record with.
