You are right to not want to run multiple DHCP servers on the same network, that can end up giving very random results.
Right now it sounds like you have both wireless routers plugged into your main router by their internal ports, using them basically as access points instead of routers (just getting the wireless users connected into the main network and letting the main router do the real thinking).
If the wireless router the students are on allows you to setup your port blocking rules to specific addresses, you may be able to on that one set it to block all communication, then allow specific rules to your internal servers. Then connect that router to your main network by the Internet/WAN port on the router and enable DHCP on it. That will make it so that the students are segmented on their own network and can only access your main network routing through the wireless router, which has the rules setup on it.
So, you would have:
Internet Connection <-> Main Router WAN Port
Main Router Internal Port <-> Teacher Wireless Router Internal Port
Main Router Internal Port <-> Student Wireless Router WAN Port
Anyone connected to the main router or the teacher wireless will be in one network and have normal access. Anyone connected to the student wireless will be in another network behind the student wireless router and be subjected to the rules setup on that router.
Otherwise, you'd want to look into setting up a DMZ to separate the students from everyone else, then setup your specific rules they are allowed to do. Your current equipment may not support this, your main wired router would be the one to look at.
Stick to your modem.
Then get an Mikrotik 750 o 450 or one of their G counterparts to do the routing for you. The modem stays working as modem only.
Then natuarllly you betterk now what you are doing - that is higher end pro stuff.
Best Answer
You can leave things exactly as they are if you want, there's no harm - but no easy way of using both links though. The other thing to remember is that those laser links, though great, are not 100% reliable, so leaving the existing setup in place means people would have the same connectivity they have today if it got foggy/snowy.