Attacking them from behind only works in the second stage. There are so many rooms in the first one where you can't enter the room without instantly getting spotted by them, starting the timer and screwing up your exploration. So yes, I maintain that it's just a frustrating experience.
Starting the timer does not screw the exploration, your fear of stupid invincible NPC does. You can literally do whatever you want as long as you care to check the boss position on map and avoid it. Also, if you escape to previous level from boss, you are getting 0:30 time again for free. So, if before you managed to clear the path to next level for not being seen by basic enemies, you'll literally get 1:00 this way on any two levels. My record was having ~3:30 by the time I got to second boss.
Also, if you hide in box after being seen and escaping, enemies tend to return to their positions looking into the walls with their asses out waiting to be stealth whipped. Also, if you do manage to melee whip them from stealth behind initially, the timer doesn't start. Aim for the head for bigger damage.
Traps are stupid and only dangerous if you're unattentive. Spikes nor crushing walls never do me any damage because I activate them with stealth stepping nearby. They only do damage when striking, so running through them afterwards is absolutely safe. In fact, as kind of spicy experience you can get enemies down on the spikes, so you can fuck them while their bodies gettin pierced by spikes. Just remember to cum right after the spikes strike, this way you'll have time to get off without getting hit with next strike.
But initially when you don't know any of this, you are simply scared. I understand that. Especially if you got bad luck with generating the first dungeon levels.
But all in all, the game is ridiciously easy if you react to any threat with correct and appropriate tactic. And if you sell your free blessed seed (given to you in a chest right after tutorial) in order to buy shotgun with ammo and some stamina like this clever guy described here several pages before, the initial character buildup virtually turns into a speedrun as 99% enemies don't shoot and are stupid as hell.
Stop being scared and start whoopping those asses. It is them who are locked in these dungeons with you, not you with them.
And that's why this game is truly magnificent. It has challenging variative gameplay, unlike absolutely most of h-games.