It depends on exactly how tough these "tough supernatural types are."
First, let's establish a baseline target with 0 endurance and no special powers or stunts. To take them out it one blow, you must deal at least 15 stress (Mild + Moderate + Severe + length 2 stress track + 1) or 23 if Extreme consequences are taken into account (in my games, nameless mooks NEVER take Extremes, and often don't even take Severes before they go down, depending on the difficulty I designed the encounter to be).
So, if that bad guy is defending from zero due to ambush, and the player is attack with a +5 skill, two maneuvers to tag, and a Weapon rating of 5 (from strength + a big sword or whatever), that's 14 stress on an average roll. Add one more tag, fate point, or bit of luck on the dice, and you've got an instantaneous kill.
Now, most worthy opponents will have Endurance scores and often Toughness powers. This can increase the stress needed for a one-shot kill by anywhere from 1 to 13 (e.g. Endurance 5 adds a Mild and 2 Stress, plus Mythic Toughness gives armor 3 and 6 extra Stress boxes).
What do these numbers all mean? To me, they mean that an assassin who takes time to catch his opponent unaware and set up maneuvers CAN do a one-shot assassination reasonably well (it's even easier if they take a stunt that increases their damage output against ambushed targets). Against something with Inhuman or better Toughness powers, though, you probably will need either the Catch or a large stack of fate points to make it happen.
Is it "too hard" to do a one-shot assassination in this game? Maybe, maybe not. I feel like the difficulty of it is just about right for a game that's more about narrative and overcoming obstacles than it is about gleeful murder. And remember that even a target who survives such an attack will now have three or more consequences ripe to be tagged, invoked for effect, or compeled against them, making them very very unlikely to survive the next attack.
The easiest way to adjust this, if it bothers you, is to remember that nameless mooks often don't use all their consequence slots. That's not because they don't care about living - it's because narratively, they're just not that big a deal in the overall story. Named villains, on the other hand, shouldn't be taken down in one shot. In my mind, dealing multiple consequences in one attack is plenty of reward for a PC who manages to sneak up on the big bad guy.