It's pretty hard to get rid of individual Mega Events short of removing them entirely. But it should be possible to make it REALLY hard to get by modding the file TheArtifact_MegaEventDefs.xml (which is in the Mega Events folder in the DLC folder).
In that file there is a turn prerequisite. Change it from 120 to something obscene and never reachable like 10000 or something like that and then save that file with the EXACT same file name in the Game directory of the ExampleMod folder in the Mod folder and then enable mods.
Alternatively, one can alter what The Artifact Mega Event does by mucking about with the file TheArtifact_ScenarioTriggerSetDefs.xml and then saving that (again with the exact same name) in the mod directory. But that requires a bit more work as you have to figure out what to replace it with.
Mind, I don't know if there is some upper bound for the amount of turns one can put in:
<Prerequ>
<Turns>XXXXXXX</Turns>
</Prerequ>
but that's probably your best bet.
