I don't think the system encourages this behaivour, but people
think it does.
Now i'm a fan of the KGS-system but let me explain my point with two "extreme" players.
Player A and Player B both have a stable real life rank, say at least SDK. Player A plays a lot on KGS, he has a huge game history and his KGS-rank has converged to his real life rank.
Player B rarely plays on KGS, so his game history is pretty empty and his rank is ?.
If Player B would start playing on KGS more, his rank will rapidly converge to his true rank.
Now consider both players improve their rank "offline", through study. Player Bs rank will converge rapidly to his new rank, the one of Player A not, because he has a huge game history. This is what people percieve as the systems problem. But i think the problem lies in how Player A percieves the system. If A is playing an average of 10 games/day a single game is not so important. What is a single loss if you play 9 other games that day? If A is not improving that is how he sees the games i presume. It's only for fun and the single game doesn't have that much weight on him.
But if he thinks he has improved this changes. Now he sees each win as a proof of his improvement and is annoyed by the fact that KGS doesn't weight these games as much as he does. So he creates a new account, where each new game has a much heigher weight on the rank.
The problem doesn't lie in the system but in the users. Also improvement is a gradual process it is not discrete (even if the ranks are). Especially in the SDK and Dan-ranks it takes a long time actually improve one stone. If A would keep his 10 games/day during his months of study his winning rate would rise over time. (From 50% to 55% to 60% and so on) And then when he finally self-promotes himself in real life, or has earned enough rating to start with a higher rank at a tournament, KGS has already learned that A has improved a bit. Not enough yet to also promote him, but it may take fewer games than if A had stopped playing on KGS during his improvement (what all these thought experiments of "offline" improvement seems to assume).
Player B on the other hand (an experience i had several times) has no such problem but enjoys the benefit that the system can give him an fairly accurate rank after just a few games.
I don't want to use that "2d?" account, since I feel that I don't deserve to play anyone of that strength without handi stones
I think here is where you make a mistake. First of all, the ?-mark after the rank shows everyone that this rank is not guranteed to be accurate, so your opponent knows you may not be a real 2d. You could also just open new games and state your assumed "real" rank so people know what to expect and play with the right handicap.
And if you - like me - prefer automatch, just play. Because the ?-mark also means KGS will rapidly change your rank after each game. So you will only have to play 1-3 games at fairly wrong ranks.
Since i had times were hardly played at all, i was often in the position of having each game having a heavy influence on my rank. And a normal loosing streak could easily change my stable 2k-rank to 3k or even 4k. But i knew, it would just take me one win against a 5k (which was to be expected from the next game, as my real strength was still 2k) to correct it. Sometimes i feel sorry for the 5k which would get me as their next opponent, but i always hoped i may provide him with a good learning experience.
Inaccurate ranks can always happen in any system, as no system is perfect. But KGS is good at correcting these mistakes rather quickly, which i find the best possible effect.
I also have an account on IGS but haven't played there for years. I'm a 7k there and i don't play there because it would literally take me dozens of games to correct this rank. And every lost game (which still happen from time to time) would push me further back. I really prefer the KGS-system over IGS.