This issue can't be fixed within JBoss Tools.
BIRT doesn't allow creating the OSGi framework out of a web application (see https://bugs.eclipse.org/bugs/show_bug.cgi?id=300924). JBoss AS 5.1 scans WEB-INF/platform aggressively (https://jira.jboss.org/browse/JBIDE-4971).
Try to use JBoss AS 4.2.3 until https://issues.jboss.org/browse/JBIDE-9299 is fixed. It would need to enable deploying BIRT web applications using JBoss AS 7.