Tokamaks produce large amounts of radiation, which is why they should be located far away from your colony. So if they're damaged, wouldn't some of that radiation leak from the Tokamak and damage nearby structures/units, spreading over time (like a kind of really slow, non-fatal Blight that could be cleaned up) until the Tokamak was either repaired, idled, or destroyed?
For structures, the effect of the radiation could vary depending on how much of the building is in the radioactive area. One fourth = slow degeneration like a Tokamak, one half = increased degeneration, people in the building start dying from radiation poisoning (nullified with Med Center + Med Center upgrade), three fourths or more = further increased degeneration, structure disabled (only for structures containing people; Tokamaks, Guard Posts, etc., will continue to function). The effects of degeneration can be reduced (but not eliminated) with research.
Of course, it does come with the problem of "radiation doesn't just magically disappear after a few days" but it is a futuristic game after all; maybe the Earthworker has something that can clean up and safely dispose of radioactive waste.
I'd also like to take this opportunity to point out that idled power plants shouldn't release an EMP blast unless they were recently idled (IE they have a "Shutdown" timer before they fully idle, if they are reactivated during this Shutdown sequence they must wait half of the remaining shutdown time to reactivate the power plant [so people can't just idle their Tokamaks when they're being attacked and reactivate when the danger is past]).
[size=0]Let's see how long it takes for people to realize this is a parody of Combine's ideas. Though that is kinda mean...[/size]