For apps which write a new file and replace atomically, the CoW mechanism doesn't come into play at all. The new file is a new file.
I don't understand what makes you think there's a significant risk of corruption. Are you talking about the risk of something modifying a file while the dedupe is happening? Or do you think there's risk associated with just having deduplicated files on disk?
The vast majority of apps using structured data and not block oriented data formats. A major exception is databases, but common file formats that most people work with - images, text, etc. often aren't best mutated directly on disk, but rewritten either to the same file or a new file. Without some transactional capability, mutating a file directly on disk can corrupt a file if the writer fails in the middle of the write. More than a few text editors use this as their method of saving to ensure that there is never an inconsistent state of that file on disk.
I don't understand what makes you think there's a significant risk of corruption. Are you talking about the risk of something modifying a file while the dedupe is happening? Or do you think there's risk associated with just having deduplicated files on disk?