Can you take over a NPC's home in Skyrim?
Solution 1:
I just tested this by merciclessly slaughtering Sven and Hilde while they slept in their Riverwood home.
Unfortunately (or fortunately, if you have, you know, scruples), even after death all of their chests are considered "owned": you still get marked as a thief for attempting to open them, which is a sure sign the room is not safe to store belongings in.
So no, despite what Davy Jones or any salty seadog might tell you, it's not safe to use a dead man's chest and/or store rum in it.
Solution 2:
I've taken over a witches cabin in the woods near the first town (she saw me stealing through a hole in her shoddy hut and at attacked me, which did not end well for her). Since the hut had a fast travel spot right at the door, a bed and a basement with an alchemy and enchanting table, I decided to move in.
This was at the very beginning of the game, and I've been going back there regularly to sleep, use the tables and store things in a barrel in the basement. So far nothing has gone missing, and nobody is around to complain about me taking things out of storage either. Items that were not previously stolen do not get marked red (stolen) when I put them in there either, so I see no downside.
I'm still looking for a location that has all the crafting tools in one place though :)