Disclaimer: this is based on my personal suppositions, so take it with a grain of salt.
I used this post blog as a reference - link here.
You didn't specify which SharePoint version you are using, so let's compare how themes work on SharePoint 2007 and 2010.
On SharePoint 2007 theming is achieved by switching the url sof the stylesheets registrations on the page.
As the linked page shows, this means that for example the link:
<link rel="stylesheet" type="text/css" href="/_layouts/1033/styles/themeable/search.css ........"/>
<link rel="stylesheet" type="text/css" ref="/_themes/32/search.......css.... "/>
Since you are just pointing to a different url for an existing css file, that would mean that you can calculate the stylesheets urls a given theme would produce, and then simulate the application of the theme by switching them into the page output (like another answer suggested).
The main problem here is that SharePoint generates the stylesheet files on the fly. Quoted from the reference article:
When a Theme is applied, SharePoint auto-generates the CSS and Images for the Theme on-the-fly, and stores them in the _themes folder of the site the theme has been applied to.
Based on my understanding, this means that in any given moment you only have a set of valid "css" files: the one globally in use by the site.
Given that, I would go for a hybrid approach. Create a copy of the set of themes you want to give to your users, deploy them somewhere and then reference this copy: that way you will always have a set of valid files.
The main problem you will need to handle is avoiding your stylesheet links begin rewritten by SharePoint when a theme is selected in the site collection / web site.