I was venturing the sewers under the temple and stumbled across the western section. Here I went off and after a mere 30 seconds I came across two dudes in robes(dark elves) as I approached with my Chrysamere ready and 2000 strength from super potions, one of them threw a dagger or dart at me which instantly killed me. I assume that these guys are Dark Brotherhood except that they werent wearing the DB armour, and I remeber a guard saying that they inhabited the sewers under the great bazaar. Anyways, even if they are the DB, I was wondering if there is anyway to stop myself from being killed instantly from the thrown weapon.

Dodge. Or use inviso/chameleon.

BTW those guys weren't from Dark brotherhood. They're members of the Black Dart gang

I ended up finding out that they were probably the gang after killing another guy on my way to the shrine of the dead who had black darts as well as that Barenziah said there was a Dart Gang down there. But still, thanks for the info.

If you get hit you will almost always die. There aren't very very few of the darts in the entire game, but they do an insane amount of damage, almost always one-hit kill. So either sneak and kill them before they throw, or do it for the quest. If you talk to the right person, you'll find that there's an ancient trap. Pull one of the light holders in the nearby sewer, (next to the door to that area of the sewer) and it will flood their base. But unfortunately, you can't loot the darts if you do it that way.

Amulet of Shadows plus high quality archery skills will work. Take them out one at a time.

Or if your a more in-your-face kind of person you could try using a ton of fortify health and speed potions and try rushing them.