I don't feel that
Magdalene and
Raphael are too upper-class and arrogant at all! I just feel that they're names, waiting to be used. :)
The only time I really get a sense that a certain name or names seem like something belonging to a particular class is when the name is decidedly 'name vomit' and looks/sounds trashy.
Honestly, if I were a kid, I wouldn't mind have an upper-crusty-sounding name. I don't think any of your names are untouchable in the least and any kid should be happy to be named
Raphael,
Magdalene,
Judith,
Jonas,
Nathaniel or
Miriam. :)