Adding an AssetContainer.moveAllFromScene method sounds possible. Could you expand more on your exact use case? After you create your assets in code, how are you planning to use them? Is your code already written with multiple scenes?
Beyond the vrHelper issue you mentioned, the assetContainer can also be used to load assets to be used at a later time without being automatically added to the scene.
It does seem like the AssetContainer will result in code that has been written with multiple scenes to need to be rewritten to use a single scene and multiple AssetContainers which isn't very obvious. Having the helper method you suggested could be good for alleviating that pain.
Switching assets between scenes is rather complex due to how tightly coupled each asset is to the scene when created. Adding support for that would likely be good but the change would be large and difficult to avoid breakage. Having special cases for certain objects like the vrHelper to move between scenes automatically might also cause confusion to users not expecting that behavior.
If you create a github issue for the moveAllFromScene I can take a look at implementing it when free.