Unfortunately, because synchronization involves conflict resolution, it would be a huge technical challenge to keep everything encrypted end-to-end without the server being able to read the data.
For example, if a user has modified the same document on two different computers before syncing them to the cloud (rare, but a plausible scenario), then there would be no way for the server to be able to merge the changes made by the two computers without decrypting the data. This also applies to a shared Dynalist document.
Even if there was a way to do so without compromising the security, we would still need to rewrite our sync algorithm to support both the end-to-end encrypted version as well as the regular version, which would be a burden to do at the moment.
In comparison, disabling sync for a document (or multiple documents, or all documents) is likely simpler. I would opt to implement that one first before considering the alternative solution.