Yes, they will run.
I recently switched my web site dinamic pages from ASP to JSP and installed
tomcat on IIS to serve the JSP pages.
Actually I'm in a transition phase during which I'm converting all the ASP
code to the new Java based architecture, so in this period I still have some
ASP pages
I think that the problem will be that the isapi_redirect dll will transfer
all the request to the tomcat
I haven't found documentation on it but if you can configure the
isapi_redirect.dll to take only requests with
unique extensions maybe you can do it
in your iis console right click on your web