Once again, i would like to point out that Ritsuko makes it explicit that the decisions about Unit-02 (and it's pilot) are made by the European government. From that i think it follows pretty logically that the E.U. agreed to Unit-02 getting sealed away by the IPEA as a compromise between the various factions. So by the time 02 gets put into storage, there is no reason for outrage. In fact, the lack of outrage can be taken as the most telling sign about a deal that was made with the agreement of all parties involved. Well, all parties except Asuka. As usual, it's the common man (girl) that gets the real short end of the stick.
Maybe there was some diplomatic tension behind the scenes, but i don't think that would be something crucial that must be shown within the movies itself.
Also, Brainman suggested Nerv Japan just sort of put away Unit-02 on it's own authority, and that is something that's outright denied by the movie.
How is that unclear? It was my understanding that those are the exact terms of the treaty, and were explained as such by Ritsuko in that very scene.
There is a difference between the terms "no country can own more than three Evas" and "no country can host more than three active Evangelions, no matter who owns them". The first is the restriction that was mentioned in the movie (in an earlier scene, actually), the second is what we see put into effect. Probably both terms apply, but the details of the treaty are never clearly explained, not like it's needed that much.