If I understand your question, it sounds like you are trying to deploy virtual private clouds for each student to play and have full control over. Sounds expensive and complex. Have fun.
Having students use GNS3 and Virtualbox on workstations, with the containers / config stored in user directories sounds like an easier solution. This allows the students for complete control to spin up extra VM of any type, use real router/switch images, vlans, etc.. It also allows the students to totally bugger it up and only affect their local system. If you allow external storage devices, they can even take their environment home.
You will need some decent fat workstations. I can't comment on how well GNS3/Virtualbox will run under virtual/thin workstations, if at all.