It's the default nature of DRM, If you wish to have these nodes excluded from being sent to the subsidiary systems, you can flag these nodes and exclude them while exporting out, Create a Derived property which identifies such,
In case you wish to avoid only few nodes, try Delete and Merge, I never come across and tried this, please be careful in case working on a Prod environment.
The issue you are facing is designed into DRM so if you use the native functionality, you cannot get around the issue. What you need to do is create a local property that is active/inactive boolean. A local property can have different values for the same node in different hierarchies. I think this is probably the functionality you are looking for.
Keep in mind that DRM is string driven. If I want a node to be treated differently from one hierarchy to another, I can have different prefixing for each hierarchy. For example:
Hierachy A Hierarchy B
I can logically treat Branch1 as the same node but to DRM it is different. What I do to it in Hierarchy A does not affect it in Hierarchy B. The issue here is that each hierarchy is a maintenance point. If I want this to be a common node (same node in two different hierarchies) but I want to have some properties different, then I need to create the properties as local. That would for example allow me to have a property (Active Flag) yes to Yes in Hierarchy A but No in Hierarchy B.