One of the weird quirks of cross country (and track, for that matter), is that a team can be built to win big competitions but not small competitions. At conference, a team with good depth but no stars can do pretty well because you can have runners who lose by over a minute to some superstars, but only score a few more points. At state, the point difference between those same runners can be huge.
I find this quirk of XC to add some drama and entertainment to being a fan, but at the same time, I don't really think the point of the sport is to force teams to run a gauntlet of different kinds of challenges in order to prove they're the best. The championship race is the real crucible, and the qualifiers are just a tool for sorting the teams that have the best shot at winning.
In any event, once we decide to allow individuals to compete in what is essentially a team race, we might as well let them score. It's not like they aren't adding to the scores of other runners and affecting the race already. The alternative of trying to remove them from scoring, and perhaps making them wear special numbers to identify them to competitors is also problematic because it would mean that they're REALLY not in the same race at all and are basically just getting in the way. If we're going to let individuals line up alongside full teams, we should allow them to really be in the race to the fullest extent possible.