I have noticed that buildings are incredibly easy to sabotage.

I used an assassin to destroy a Thieves Guild building, and the odds of success were 95%. Naturally, it worked. For balance purposes, is this fair? Is it realistic? I shudder at the prospect of having a late-game barracks which cost me more than a cumulative sum of 45000 florins suddenly destroyed because some assassin with only 1 subterfuge went in and set a match to it.

If you look closely, you'll see that a building is rarely completely destroyed in one go...

As a matter of facts, even if the building is 100 % destroyed by sabotage, it is only a matter of repair and it will be as new in the next turn in exchange for somme of your cash and furtunately not the 45000 $ it cost to build it and its upgrade...

Righty. That confuses slightly... can they be fully destroyed then by sabotage?

You can destroy it "100%", but that doesn't mean that the building disappears... It just turns red, and will be useless until you repair it.

BTW, if you put a couple of spies in a settlement, the chance of a successful sabotage DRASTICALLY decreases.

Oh, and church buildings are the easiest ones to destroy... 80% at 1 subterfuge, 95% at 2, if I remember correctly.