I am using JBoss 5.0.1 default configuration for my deployment.
Several JBoss AS services use the DefaultDS data source defined by the hsqldb-ds.xml file. In order to remove that file, you need to replace the DefaultDS datasource with something, which is usually some other data source. One thing you can try is to remove the services that need that data source. This would include messaging and the ejb timer service. Do a text seach for DefaultDS in in all XML file to locate all uses.
As fas a replacing the connection pooling built into JBoss AS and used by the various AS services, you are on your own.
On the other hand, if all you want to do is handle your own connection pooling for your own apps, then all you have to do is not define a *-ds.xml file for your database.