I've created a custom user profile and attached it to a user type. When I do a GetUser and tell it I want the profile properties, is there a mechanism to map this data to a Glass model, or is this better handled strictly the "Sitecore" way?
Glass mapper is for mapping Sitecore items to Glass models. That's all it was designed to do. Don't try to shoehorn it into mapping things it wasn't designed for. Just use the Sitecore API and create a model.
If you really must use a tool to do the mapping for you instead of just writing the code. Then have a look at AutoMapper, that is designed to map from one model to another. But if you are only doing this once, I'd say the overhead for that is not worth it.