What are the complaints these people have? They've solved all challenges within their skill level and therefore cannot compete with people of similar skill level who also have some dead sites linked? ;)
In the end this is a question about what the scoring means/reflects and adding another clause to it. If you ask me, the scoring is already arbitrary enough. Personally, I'd much rather see time spent on getting a well-constructed scoring, instead of duck taping another feature onto it. (But I guess this has turned into a pet peeve of mine. :P)
Looking at it from another angle: why would past achievements get worth less? Taking it to an extreme, let's assume we have an old challenger that has only old dead sites linked. By this time, his score is practically zero. Now a new challenger comes along and linkes a few newer sites, giving him roughly the same score the old challenger once had. God, in his hatred for hackers, kills the servers of a bunch of hacking sites, including all the ones the new challenger had linked. We are now left with two challengers who, in terms of original score, have achieved the same, are only linked to dead sites and yet one has much more points just because he got them more recently.
Is it really that unfair to keep the score? Isn't it also unfair that some are older and got a head start on gathering these valuable points? How about people that simply have more time to spend on doing challenges? Etc. :)