I've always loved the name Stephan for a boy (Steff-an). Do you think everyone would misread it, and therefore mispronounce it, as Stephen? And just WDYTO the name?
I really like Stephan pronounced stef-AWN. I wouldn't automatically think it was Steff-an though. I'd be much more inclined to say stef-awn or stef-AWN. I don't think everyone will misread it and mispronounce it as Stephen, but if you're worried, how about spelling it Stefan?