Yes!
Foundation swatches generate CSS. Since CSS works on any website, swatches can be used in any theme/framework.
There are some exceptions though...
I would not recommend using Site Styles. It does have a lot of very specific features made for Foundation. You can use the Swatches stack instead.
There are also many swatches that are made specifically for Foundation components: Menus, Component Colors, Top Bar, etc.
Many swatches allow you to use the predefined colors from Site Styles. These will not work in other themes as well. If you know your stuff, you could replicate these features with the Custom Color swatch from the Swatch Pack.
So you will not get 100% of the functionality in a non-Foundation theme. I would say that you get around 90% though. Not too shabby...
Why not sell swatches outside of Foundation?
I thought about this and almost sold them as a separate product for non-Foundation users. However, for the price that I would sell them at, it just didn't make sense. It's better to just purchase Foundation and get all of the benefits. Or just use the swatches, it's up to you.