To handle this problem, go to your Advanced preferences, and re-enable all the options under "Scripts & Windows", except "Open a link in a new window" is unnecessary. (Others may not be necessary either, but I'm playing it safe.)

Unfortunately, these values don't seem able to be set on a per-site basis at this time (1.0), so you'll have to toggle them on and off as you want them. Alternatively, you can set up a separate Mozilla profile for using LON-CAPA.