"Since its a University we can not let every schools running its own moodle with no standardization."
What do you think of as "standardization"? Why can you not let them run their own Moodle - to a point?
You can allow the schools to each have their own independent Moodles, and there is an increasing amount of documentation onhow to do this. I understand that in the near future set for v2.3 is going to be the opportunity for "multi-tennating", that is, precisely the sort of setup you are talking about. Administration remains central, but each school is responsible for its own content, its own usage and its own look. You can input to content, which would, I think, be helpful in a pedagogical sense, and tie the schools even closer to the universty. You can look at this discussion to get started...