Sorry that I can't give a more encompassing solution--all I can really offer are my personal views and opinions.
Though my view may be biased, I don't think any stats-minded player wants to see their points wiped, even if everyone else's are eliminated as well. From my perspective, the major two problems that the stat system has are similar to ones you outlined HeK. First off, players are not explicitly awarded for simple activity (or conversely, penalized for lack of activity). I won't deny that any of the top 50 players are amazing players, but perhaps keeping inactive players there doesn't properly reflect the active server community. Among at least three people I know of in the top 10, "passing Raheem" is regarded as a truly formidable obstacle, haha. A simple remedy for this would be to either simply award players points over time as they play, or penalize points from players that have been inactive for a set period of time (a week? I dunno). Since I don't know how the stat algorithms work, I don't know what the implications of either option would be in the long-run.
On that note, let me address the second point, easily the one you hear myself, among other people, bitch about the most. I understand that players in the upper echelon of points should have a more difficult time gaining, or perhaps even retaining their points. However, the way the system works now has several seriously negative implications. I believe that these problems are rooted in the problem that DarkChief already outlined. It's playing with pubbies. If you'll let me elaborate from our experiences, Liquid and I have had numerous encounters where a player new to the server (and thus having a low number of accumulated points) will get the drop on us and kill us. Or perhaps competitive-level players will hop into the server to play casually for a bit and kill us fairly consistently. I certainly have encountered players that I have never seen on our server before that were clearly more skilled than I. As a result, the game awards maybe 50-100 of the high-score player's points to the "new" player (if you're unfortunate enough to be killed via melee attack or unforeseeable taunt kill, 200 or even more points may be stolen--so I believe). I know that it's supposed to award supposedly new players for killing supposedly more experienced ones, but it seriously can start to affect the latter's perception of the stat system, especially when he or she considers the stark difference between playing with "pubbies" and with server regulars. One could argue that the system
penalizes players for gaming with unfamiliar people, which really shouldn't be the case. This may even encourage players to avoid playing at times other than when the server composition is all-regulars (IE Team Fortress Tuesdays, Friday Night Fights). Sure, it's partly the fault of the player for being somewhat petty about what is cosmically a meaningless value, but I don't think the stat system should produce an environment where this could occur. My only real suggestion for remedying this exigence would be to either put a cap on the amount of points that could be stolen (maybe 30?) in a single kill.
Perhaps a system could be implemented that completely ignores the skill difference perceived through point difference, although this system really would only favor higher-point players, so forget that actually.
Also DarkChief thanks for showing that session function of HLStats that I didn't know about. Now I can wretch over a session I had where I was 1.9 kdr and -1140 points
EDIT: And sorry if any of these changes have already been implemented, or if my information regarding the algorithms is flawed.