I've downloaded a sim that comes packaged with a geneticized/townified skin which I don't want. The only problem is, I've already created and placed this sim in my neighborhood, and I'm under the impression that deleting any custom skins/eyes that are included in the genetics of an existing sim will bork my game (or at least that sim's DNA). If that's the case, I'm fine with that sim alone keeping that skin (I don't plan to let her have any kids anyway), but I don't want this to spread to the rest of my gene pool by being geneticized/townified.

I can't find any tutorials for how to de-geneticize/townify a skin, only how to make it geneticized/townified in the first place -- do I only need to reverse the process to make it a custom-only skin again? Or are there any other additional steps? Or is there any other method I can use to avoid having the skin spread among my other sims?

You need SimPE to change her skin to another skin. Either Maxis/default or to another custom skin. You need to open the sim, go More, Sims DNA. In there you will see under dominant the skin that she has on now. Delete the long code there and replace it with the code for the skin that you want.
http://www.lothere.com/verso/page/16 Once you have changed her skin you can delete the skin file that you downloaded.