I dont think so, you can remove inherited attributes- this just violates the OOPS. Either the attribute need to move to specific storage class or if the storage class is same for both BOs, then You can hide them in the subclasses, so that it wont be visible in teamcenter.
as @rajesh_arumugam said, OOPS concept is fundamental to establishing and driving references and relations within Teamcenter.
Probably this approach might help in your scenario:
On your parent class, set the propertyconstant 'visible' to 'false' for the properties you don't want to get bothered about in child classes (even though the property is inherited in child class it is invisible by default).