I do not think it is a problem for a few reasons. Kin'as sofrim tarbeh chochmah (jealousy among scholars will increase wisdom - Baba Basra 21a). A certain extent of competition in Torah is a good thing. Having people compete for even something as minor as points helps increase Torah and wisdom. There is an issue of a person becoming haughty or seeking honor because of his Torah knowledge, but I don't think this specific site would cause such a problem. This would probably be the conversation:
High-ranking user: Give me lots of honor.
Regular guy: Why?
HRU: I have 1000 points on Judaism.Stackexchange.com.
RG: On NASDAQ or NYSE?
The point is, no one is getting too much crown or glory from this site.
The commentators actually explain that Mishnah based on a Gemara in Nedarim (62a) that a person shouldn't learn so as to be called a sage or rabbi but he should learn out of love. I do not think that people are only learning Torah so they can know enough to answer questions on this site and get a high score. Even if that would happen, I think we would apply "לעולם יעסוק אדם בתורה ומצות אף על פי שלא לשמה שמתוך שלא לשמה בא לשמה". Ideally a person should learn lishmah, but he should use whatever motivations he can to learn before he's at that level.
The way I see reputation points on stack exchange is that they are useful for the people asking questions, not for the person getting the points.
That is, when someone comes to the site and asks a question, seeing the points next to a person's name gives that name 'recognition status'. If there is a debate between two people, one has 1 point, and the other has 10,000 points. You might err on the side of the person with 10,000 points because they have 'proven' themselves.
Since the points, (I think) are intended to help people weigh answers, I don't think they count as a crown.
If however you are using the points as a crown, perhaps its a good idea to question yourself.
One argument that it would be "a crown to magnify yourself": the "Association reward" that a user recieves when they reach 200 reputation points on any stackexchange. Namely, they automatically get bumped up 100 points on any other stack exchange they join, in order to get them past the "basic user" stage, as they have proven themselves to "understand" the stackexchange community/style. I can imagine a person doing that on judaism.stackechange because they feel it is easier for them to get to 200 on MY than 100 on mathematics.stackexchange, and they want to be able to comment on posts, etc.
Making the Torah a crown to magnify yourself with isn't refering to how other score you. If you share knowledge and help people with it, it just shows the appreciation of the other and the value of the answers that been given. It is about the opposite, that someone would put on a crown (give himself a status/might) based on his or her knowledge of Torah to show off with it, place himself on a footstool and being arrogance, presumptuous or highhanded about it. A real rabbi is a real teacher, and a real teacher is teaching Torah not for his own benefit, but for the benefit of others, not out of love for hisself, but for the love to teach and out of the love for others. Although thats just my opinion.