AFAICS, the "ORB not found" exceptions begin just after:
2011-01-05 11:40:45,432 INFO [org.jboss.web.tomcat.service.deployers.TomcatDeployment] (RMI TCP Connection(4)-10.11.1.112) deploy, ctxPath=/webapi2
2011-01-05 11:40:45,449 INFO [org.jboss.web.tomcat.service.deployers.TomcatDeployment] (RMI TCP Connection(4)-10.11.1.112) undeploy, ctxPath=/webapi2
which kind of suggest me the app is beeing undeployed. Also, all the exceptions are "... during stop for...".
Regarding cleaning removing the webservice module from the app server, that's not easy with AS 6 (things are going to change here on AS 7). The only solution I can think about is creating your own server profile without the webservice stuff, something in the middle of "minimal" and "default" profile. But that's not straightforward for sure.
It's probably faster for you to comment out the @WebServices annotations (assuming you're using EJB3 endpoints only) in your sources.