Hi Tim -
What about modifying the BaseX web.xml in $basex/webapp/WEB-INF? That was you'd be disabling in Jetty instead of Apache. To be honest I have no idea if this will work, but:
<servlet>
<servlet-name>default</servlet-name>
<servlet-class>org.eclipse.jetty.servlet.DefaultServlet</servlet-class>
<init-param>
<param-name>dirAllowed</param-name>
<param-value>false</param-value>
</init-param>
</servlet>
or some variation thereof? I cribbed this from stackoverflow, naturally (and here's where I found it: [1])
Hope that's helpful, apologies if it's only noise.
Best,
Bridger