you can re-push the app butt...
If the service is disabled and stopped there is not way for the app to recieve the repair type push. It will not re-install because it will see the PC as already having the client installed on it and will ignore any subsequent installs.

My logon script so far works as I want, in that it will check to make sure the client files are not deleted, if they are it will force a re-install of the client. So half my battle is done.

Now I just need to re-enable the service. I am working on doing a snapshot of the PC before/after the service is enabled/disabled to see if I can use that instead.