I am developing an application using the ASP.NET MVC platform, which will be exposed as a service over the web (the SaaS model). I am trying to determine the best way to partit
Sound like option B to me. It's the only one that seems to a) work with your architecture and b) work with your potential future goals. You can make the price of the SSL cert for the custom domains part of the start up cost for the service (or amortize the cost over the monthly charges).
I don't see a real difference between A and B, they're effectively identical save that you CAN use a wild card cert for A, you just don't HAVE to. Without the wild card aspect, A == B, the fact that they're all subdomains of example.com is coincidence.
Even with option A at the beginning, you have room later to expand to option B if that's the kind of service feature you'd like to offer your clients.