Concerning the busy count - do look at [this](http://msdn.microsoft.com/en-us/library/system.web.hosting.hostingenvironment.incrementbusycount.aspx)

On Application_End, you would want to do process.Kill(includesChildren: true).  This api is available in Kudu and might need a little tweak to work here.   Still, we have to address w3wp crash as well as publishing flow.