Explain the problem as you see it
Deleting the supertag template's children nodes (not Fields) will delete the rendered children from instances (and it seems that the added "grandchildren" nodes in instances won't be moved to trash but vaporized).
Why is this a problem for you?
I find this behavior could be haphazard if users aren't fully aware it is an inherited structure, not a cloned one (which I didn't in the first place, although the colored bullets help).
While it is the same case for fields, child node structure is probably more human error-prone since they are not commonly inferred as part of the schema.
Suggest a solution
While I think the inherited model makes sense, and I preferred it that way (evolution in the schema will be applied to all instances), it could be implemented in a way accustomed to users' mistakes, like leaving the rendered/cloned nodes in the instances but detaching them from the template.