Youtube lately is full of videos with titles "Pure stealth", "100% Ghost" when refering for example to Dishonored or AssCreed games.
Just compare that to Thief playthroughs on expert.
At least Dishonored is pure FPP. The AI's ability to counter stealth is a bad joke, though.
Anyway, the main problem with "stealth" takedowns is that generally it's better for player to remove a threat once than to have to avoid it repeatedly.
If, in a stealth game, you give player tools to dismantle the whole security structure of a level without reacting as player does just that, you quickly no longer have a stealth game.
What you need to do is to counter-incentivize leaving security structure - patrols, security measures, lighting, etc. - alone if possible, to encourage player to devise and implement plans involving only minimal changes, and to react to their repercussion.
A level cleared of patrols shouldn't be the safe level for player to move around, it should be an obvious situation to whoever has posted the guards in the first place resulting in teams knowing you are there being specifically sent to find you - agressive, proactive and alert, as opposed to bored and reactive, also likely better trained and equipped than the regular guys.
Player should be conditioned that doing *anything* that may allow someone to infer they were there is a potential failure mode. In a true stealth game altering the state of the level should be similar to taking hits in a combat focused one.
Leaving the antagonist's stronghold with all the guards patrolling, all the doors in the same position as before you entered, all torches lit, all windows unbroken, no spent accessories left behind and only a copy of antagonist's plans (with original being safely locked in its safe) in your pocket as a proof you actually were there should be the perfect completion game measures you against.