The best thing will be to remove the Sims and also remove the custom skins. I'm not sure how to remove the skins, but I'm sure a more technical member will be along soon.
It can be risky downloading from the Sims 3 Exchange because you really don't know what someone is putting into the files they upload.
True, but the main reason I do it, is for the pretty hairs...xD
The Sims hairs tend to not blend the highlights, tips and main colour all that well, and I like to play with my sims by giving them crazy coloured hair, and the styles never seem to work. Therefore, I get custom content hairs. Only thing is, with the way the skins are on the Sims 3, the skins tend to replace the ones already there. Plus, some come with crazy content that can affect, all sims from babies to elders which irritates me, because then I get glitched babies.....
Anyways, I would have no problem in removing the sims, if they didn't take all of the other custom content with them.