According to Apple Support documents, personal domains will be kept intact with MobileMe. Blogger Sean Sperte noticed a "personal domain" option while watching the MobileMe quick tour. That prompted some investigation which led to this support document. Sure enough, it confirms that .Mac personal domains will remain untouched by the change:
"...If you have a personal domain setup for your iWeb site, it will continue to work without changing any settings at your registrar."