The AStyle way is not so bad actually, it is simple and it works. But there are just a few things which AStyled does not do the way I like it (for example, it compresses white space in comments and around '=', and always puts {} in a new line, so if you spend a lot of time laying out things properly, the code formatter destroys it later). Also you can only configure everything from hand, or nothing, which is annoying (for example, I like the way ANSI style looks, but I don't like spaces for indentation).
Why don't you make a simple "choose one out of n" interface (list box, for example). The actual configuration is read in from a config file, and you just provide 3-4 such configs. If somebody wants something different from ANSI, Gnu, or K&R, then he can write his own config and is not limited to a stiff GUI. Most people will use one of the default sets, so they have a 1-click configuration.
You could use tinyXML for the parsing, so you save an awful lot of time on designing a GUI (designing a GUI takes 90% of your time, but only 10% of the people use it 1% of their time...).