If I were a passenger on a plane that broke down and failed to clear the runway, I wouldn't be cheered to know that heavy jets would be landing over me or behind me, and that all I could do was trust that they wouldn't hit any 'bits' on the runway (say, left by a plane that had a problem on landing) and blew a tyre. Isn't there an issue of passenger protection here?
I think passengers are normally removed/evacuated from aircraft that are going to be stuck on a runway for some time, plus the remaining runway would be checked for 'bits'.
You may be interested to know that it is standard procedure in the UK, if the weather and runway length allow, to have an aircraft touch down before the previous aircraft that landed has vacated the runway. This is a much more dynamic situation than having a stationary obstruction at a known distance from the threshold but it doesn't seem to raise many questions.
Passenger aircraft operate in/out of airports with a large variation in runway length, width, slope, altitude, surface friction, etc. There are established methods to calculate the required stopping distances and to add a safety margin to these. What's beyond the end of the runway, once you have taken "stopway" into consideration, is fairly academic. There is only a certain amount of "what if?" you can reasonably do: for example, 09R at LHR has a dual carriageway and a petrol station 4-500m from the far end... This has not, to my knowledge, stopped anyone taking off or landing.