If your existing application can take advantage of the many existing modules for DotNetNuke, you may consider refactor it, use as many standard modules as possible and concentrate you dev. efforts on the 10% with you business logic, bye learning how to develop a DNN module.

On the other hand, if your business logic is 90% or your app and will ever be, I wouldn't switch to DNN. I don't see how MVC might help you either since you say that separating the presentation and the logic would be time consuming (which is precisely what MVC tends to) - a can imagine a painful refactoring.

If you start from scratch with a heavy database app and want a clean MVC architecture, consider Ruby on Rails but bye bye to the great collection of modules that DNN can provide.