Other app servers support anlternate run-as semantics from the container init/destroy lifecycle callbacks. Weblogic for example:
http://e-docs.bea.com/wls/docs81/webapp/weblogic_xml.html#1041058

This is an equivalent of <run-as> for init method for servlets. For example:
<init-as>
<servlet-name>FooServlet</servlet-name>
<principal-name>joe</principal-name>
</init-as>

<destroy-as>
<servlet-name>BarServlet</servlet-name>
<principal-name>bob</principal-name>
</destroy-as>

This would allow more control over how these methods interact with secured resources. Similar options could be added for ejb lifecycle methods as well.