I could totally picture some uninformed person draining a node without realizing it, and causing their spawn town to become full of angry zombies and floating tazer-balls(Or simply burnt down by lightning). Imagine the carnage a dedicated griefer could cause with a bunch of arcane bores. Destruction of bases and TC mobs everywhere. Luckily it takes a lot of research to get that stuff, and griefers tend to be the "instant-gratification" type.
lazy extra stupid griefers yes.
real serious type griefers write their own client mods. research tree? pfft i haz the equivalent of worldedits worst plus creative when it comes to ruining the universe. then again if your server doesn't have multiple backups and instead re-overwrites the same backup each time, or worse has no backups, your server is run by a lemming with drain bramage anyway.
backups. frequent independent backups. they cure cancer, viruses,turn griefer visits into nothing more than service hiccups and more, but most people will not take the time.
furthermore as one of the fun hacky tricks involves hijacking the session of someone who is afk and idling for an extended period, the hijacker/griefer would have access to whatever that user had access to research wise even aside modded client gobbledygook.
this is actually one of the more amusing things one can do. icbm and simply port premade maps over mystcraft ages for the battles. later simply overwrite the age folders with clean copies. actually i think i've come to the conclusion that map porting functionality is the most amazingly useful thing in the universe added by mystcraft.
as to other issues isn't warded stone/glass still immune to pretty much all the icbm missiles? can't recall if the redmatter missile had an effect or not.
combo mffs and tc3 and yes your base can be immune to external access afaik. just leaves worrying about twilight forest and nether portal spawning access to the inside from the alternate dimensions. build in the same places in those dimensions to prevent this.
lastly if you know of a way to remove tc3 warded stone aside from wand turtles, please pm me. i know pulsed block breaker mffs fields layered on the warded stone can eat turtles and frame machines and pistons that may attempt warded stone interaction but leave the stone intact.