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Here is an untested
Here is an untested theory:
First log in, or use user.login();
Then try possibly calling:
system.setVariable('site_offline',1);
As far as modules, I think a new service would have to be created to enable/disable them. Sounds fairly simple in theory. It could be as simple as flipping a switch in the mysql system table. But I'm not that advanced in drupal enough to know.
try the maintenance mode and let us know!
Matthew Connerton
http://www.mrconnerton.com