I am not sure who decided to change how services get overwritten in 10.2.1 but I do not think this new method makes things any better. It actually adds extra steps if overwriting a service with an existing cache.
Often times when building a map document for a caching operation you use group layers to help symbolize data at different scales. Although after the cache has been created you wish to simply your rest endpoint by removing the group layer and only including the layers you wish to query or create pop-ups/identify. This makes it easier for developers who are using your services to write applications against.
In 10.1 SP1 we had the capability to overwrite an existing service with the option to "KEEP EXISTING MAP CACHE. Now when you overwrite a service at 10.2.1 it creates a new folder structure in your REST endpoint and a new cache. This seems counterproductive to me and I truly do not understand the logic, although if someone can explain how this makes things easier I would be willing to listen.
I would like to request that the option still be given to overwrite an existing map service with the ability to keep the existing cache. As it is now I have to manually copy the cache from one location to another, this extra step seems like it could be avoided if Esri would give us the method back that existed in 10.1 SP1.