All deployments are metadata / attachment driven via deployers.
What this means in more human form? :-)
btw: did you read any of the DZone article's on Microcontainer topic?
Each configuration file is transfomed into some metadata class / instance.
And this metadata instance is added / attached to DeploymentUnit instance.
DeploymentUnit is what is passed between deployer instances -- see Deployer::deploy(DeploymentUnit unit).
DeploymentUnit's attachments are nothing more then a smarter semi type-safe Map.
As you can see deployers actually don't care where this metadata instances come from.
It could be either from parsed configuration or added programatically.
So, to answer your question, yes it can be done programmatically.
Simply add a new custom deployer to the existing chain of deployers.
Where you would add or replace or modify an existing ClassLoaderMetaData, which is jboss-classloading.xml is parsed into.