*During the startup phase, I have some code that checks things like environment status, remote resource availability, etc...

How can I initiate a clean shutdown at that time?*

You need to write an MBean and in its startService() method you start a non-daemon thread which invokes System.exit(-1).

   // The lifecycle
   protected void startService() throws Exception
   {
      log.info("Starting with message=" + message);

      boolean problem = false;

      log.info("checking some stuff...");
      //...

      log.info("oops found some problem!");
      problem = true;

      //...

       
      if(problem) {
          Thread myThread = new Thread() {

              public void run()
              {
                  log.info("Shutting down");
                  System.exit(-1);
              }
          };

          myThread.setDaemon(false);
          myThread.start();
    }
   }

The source code is attached.