You know, this whole idea with the marker files, I think it's just to complex for a simple deployment. If one is truly interested in deploying in a safe way, they could use the CLI, no?
Or, why not turn the problem upside down?
Treat the deployments directory exactly like in previous jboss versions (i.e. deploy something when is copied, undeploy when is removed) to retain backwards compatibility with user expectation, tools and the like.
In addition, if you want to go for an atomic deployment of XXX (packed or unpacked), create first a marker file XXX.skip, then copy in the deployment (packed or unpacked) and remove the XXX.skip file when done to trigger the deployment. Voila.
To undeploy either remove directly the deployment, or if you fear it cannot be done atomically, create again a XXX.skip, remove the deployment and then remove the XXX.skip file to trigger undeployment.
For a re-deployment just touch the packed file, or the directory in the unpacked case.
This would ensure atomic deployments, while retaining "backwards compatibility" for the ./deploy directory notion.