[eluser]boony[/eluser]
Hi,
We chose CI as the PHP framework of choice at our institution last year (Diploma Website/Software Development) and it has been a great success. Overall, I think the students have easily taken it up and the learning curve is not very steep.
Students have all got individual server space on the university server but we haven't gone into the full access issues that you mention. Not sure why there would be any problems with what you want to do.
My personal thoughts and feedback from students is that this is absolutely the way to go and I would not hesitate in supporting the choice.
Good Luck