That’s correct.
Mutation is a different from deletion operation. It is possible to merge, but very infeasible in the medium term. It may never be supported for being complex (due to transactions feature) and very simple to handle via client application.
One thing you can do is create a “Deleted” Label via mutation. Thus the node is not actually deleted, but identified as something to be deleted by application. After that you can create a worker to hunt these nodes and then delete them in a single operation.
And your queries you can always add a filter with “@filter(NOT has(Deleted))”.