You need to give the fake artifact to Braniess. Kym then thinks you gave him the real one - let her think that, and put the real artifact back on the pedestal.

IMO it's completely retarded that offering a suicide pill to an alien who threatens your life with a gun is completely retarded, since it's basically a form of self defence at that point (technically it's not even that, since you didn't actually kill him, technically speaking). And it's not like the game takes into account all the people on all the space ships you destroy (apparently killing people in space is irrelevant for being a good guy).

Unfortunately this bizarre situation still exists (I actually thought a recent patch changed this - to basically work exactly how you described above, i.e. the "good guy" part relates to the artifact only, and not whether or not Brainiess kills himself by eating your pill).

I am of course assuming you're playing with the latest version...