I read through all other community posts and internet before coming.
I have an MSM with master pages setup. While i have created live copy pages and deleted the one of the child item in a container by breaking the inheritance, i am getting my current component converted to "wcm/msm/components/ghost". That is fine as it will help us in re-enabling the inheritance but due that it is causing problem in Publisher as well since it is getting extra <div class="ghost <my-comp-name>"></div> since by default all childs under the layout container are getting pulled..
As you said, MSM ghost node is needed in author for re-enabling inheritance in future.
In publish, as you are listing the resource items from LayoutContainer, you can write a custom implementation of LayoutContainer using below actual implementation as sample. (mapping it to your component resourceType in @Model annotation)