does "natually"here = "naturally, the door creaked?"
The basement door creaked. Naturally, she thought, and hooked a finger in one of Eli’s belt loops as he started down. “So we don’t get separated,” she said when he glanced back.
“It’s not the Amazon.”

Question

does "natually"here = "naturally, the door creaked?"
The basement door creaked. Naturally, she thought, and hooked a finger in one of Eli’s belt loops as he started down. “So we don’t get separated,” she said when he glanced back. 
“It’s not the Amazon.”

Answer

Naturally here ... could refer to the woman's response the the door creaking. She naturally hooked her finger and said "so we don't get separated". 
Often when doors creak people  look toward the direction of the door... or have a response to it... at least that is what I do LOL

But it is a little bit difficult to tell. Could you write out more of the passage? ( before this portion)

Answer

It means that she thought "of course it would do that right now" in a way that means she wished that the door hadn't creaked.

Answer

Yes :)