Is it ever "legal" to steal from a slain enemy's home?

A few times, I've had to vanquish an enemy in their home.

Most recently, Nepos the Nose.

However, even after they're defeated, all of the possessions in their house are still marked as "Steal" instead of "Take". Are there still negative consequences for taking things from the houses of a slain enemy?

No, it is still not legal even if the owner is dead. Taking those items will still mark them as stolen in your inventory. However, since there are no witnesses left, you will probably be able to get away with it. On top of that, you are probably unlikely to be the target of some payback by the now dead owner.

Having said that, the only place you can sell those stolen goods is still through a fence (which requires joining the thieves guild). And the items will still be taken away if you are ever arrested on some other charge.