Before we address your question, we should ask a basic question: How did the behavior of Rebbi Zecharyah ben Avkulas express the Midah of Anivus? In what way was he acting with humility? The Chachamim wanted to accept the sacrifice of Bar Kamtza even though it was blemished and he discouraged them because people would have a mistaken understanding of why they did that. Then they proposed killing Bar Kamtza and again he discouraged them for similar reasons. Where is the humility here? I believe Rashi is bothered by this question and answers that Anivus means Savlanus, the willingness to tolerate other people. This seems to be Rashi's central definition of humility. Rashi commenting on the verse that describes Moshe Rabeinu as the most humble of all men (Bamidbar 12:2) says that he was "Shefal v'Savlan."

We get an insight into why being a Savlan is so important to Moshe's leadership of the Jewish people when Moshe asks Hash-m to appoint a successor (Bamidbar 27:16). He addresses Hash-m as "Elokei ha'Ruchos." Rashi explains why Moshe used that particular name: Hash-m understands each person's particular Da'as (mind) and he should appoint a successor to Moshe who can be Sovel (tolerate) each individual because he understands their particular Da'as. Moshe had this quality ("Anav Me'od mi'Kol ha'Adam") and he requested from Hash-m that he appoint a successor that also possessed it.

Applying that to our case, it means that Rebbi Zecharyah expressed his humility by showing tolerance for Bar Kamtza despite his treacherous behavior. Rebbi Yochanan says that this was the wrong time to use this leadership quality. Even Moshe, the greatest Anav, who could try to make peace with his arch enemies Dasan and Aviram (Bamidbar 16:12, Rashi), knew when it was time to stand in the breach and punish the wicked in order to protect the Klal.

Now to answer your question: I think the Rambam (Hilchos De'os 2:3) is speaking about man as an individual and how he should relate to other people, whereas the story of Bar Kamtza is speaking about man as a leader and when he must set aside his humility for the sake of the Klal. (See also Mesilas Yesharim, chapter 20, who quotes this episode as an example of misplaced conduct of righteousness.)

There is another possible interpretation of "Anvasanuso shel Rebbi Zecharyah...." The Tosefta in Shabbos (17:4) records a Machlokes between Beis Hillel and Beis Shamai regarding Muktzeh. What does one do with leftover bones and shells after a meal? Beis Hillel says one is allowed to pick them up and throw them away. Beis Shamai says one lifts up the board on which they are lying and shakes them off of it (for a fuller discussion of the Halachah, see Shulchan Aruch OC 308:27). The Tosefta finishes by saying that Rebbi Zecharyah ben Avkulas was even more careful. As soon as he was finished with a piece of food that had a bone in it, he would throw the bone away while it was still in his hand and not put it down in front of him. Commenting on this, Rebbi Yosi cryptically says the same thing that Rebbi Yochanan says in Gitin, "Anvasanuso Shel Rebbi Zecharyah...."

Here, we certainly have to ask what does this have to do with humility? It seems that, according to the Tosefta, Rebbi Zecharyah's behavior has nothing to do with the humility that the Rambam is describing; rather, it has to do with his inability to be Machri'a (decide) the Halachah. In the case of Muktzeh, he simply avoided the whole issue by immediately throwing the bones away. In the case of Bar Kamtza, he could not come to a decision about what to do with Bar Kamtza. Why is this called "Anivus"? Perhaps because he did not view himself as being "big" enough to make a decision (see the Maharatz Chayos there in Gitin who has a similar explanation).

Kol Tuv,

Yonasan Sigler