If you want people to be able to use custom styles, that's extra complexity regardless. If you let people upload their own stylesheets, you need storage for potentially millions of extra files, validation, size limits, etc. All of the hazards associated with arbitrary file uploads.

Or extra fields. Then all you're dealing with is a few more color values on the backend for a stylesheet that's already being generated by code. It's a lot easier to validate a color (the code for which is already there) than an entire nearly Turing complete language.

You could even split the difference and have themes generated from one or two user supplied colors, instead of fields for each css value.