My opinion on how to deal with uninhabitable planets is this.Have a scientific exploration landing party type ship in. Allow the ships to go from charted uninhabitable to charted uninhabitable spending X amount of turns on each to search for extreme worlds, potential mining opportunities, or find ancient ruins.
I too like this suggestion, Maybe not right away in the game, however, mid to late game maybe allow your survey ship (one most if not all anomolies are gone) to get into orbit of a "dead world" whatever type and allow it to explore/survey the planet. It may find nothing of use, it may fine an artifact that gives you something similar to an anomaly, or maybe like you suggested in rare situations find something that will be an ancient base/ruins that will turn this planet into x quality (may be an extreme world then) but makes it habitable. You could then colonize it, if you get their first. This may happen in a ratio of 1:20 or more but, make it possible.
Make it a risk factor, after all it's originally dead for a reason. So if they uncover an ancient ruins maybe it's a weapon and releases the dead "Dread Lords" or "destroys the ship", or converts the solar system it's in to a "black hole"(thus destroying the ship and anything in the system). There are many things that you could do both ways to make it a win/loose situation.
Anyway that's my thoughts on "dead worlds" Maybe a DLC titled "Dead Worlds" or expansion though if doesn't make it to base game if at all.