You can probably use both options. Give the desktop client one for a higher fee and charger less for online (or vice versa). And since you wrote it in C#, porting it to ASP.NET 2.0 shouldn't be too difficult from what I can imagine (I haven't seen your source code so it's hard to comment).
Regarding load times, AJAX is giving web applications a pretty neat work around for that (well, to some degree at least). Read more here: Ajax (programming) - Wikipedia, the free encyclopedia