Couch's design documents are protected, even though they are replicated, as you say. Unless I'm misunderstanding your question, your application will be safe from modification, as it will be update-able only by the author.
However, when the user attempts to replicate changes to another server (maybe the original source server, maybe another server not under their control) it is the validation functions on the target server that control which writes are allowed to proceed.
So if my http://jchrisa.net server only allows updates from me (for instance for blog posts), you can still replicate my blog to your machine, and edit posts there, but when you replicate the changes back to my server, they will be rejected by my validation function.
So any app written on couchapp can be considered to be modified by the end user if it's replicated to their machine. Then any application where you don't want users fiddling around with your 'source' is out of the question.
That said, there's plenty of applications that you'd want to pass along with the user's own data that you'd want the end users to fiddle with and improve.
With that in mind then, I'm guessing you can have validation functions that allow you to selectively update the design documents that you want from another person's changes, just as I can selectively replicate data from another person's copy of the couchapp.