From my understanding of copyright law, by Mojang not taking actions against mods they have given implicit approval to modify their game. Another thing to note, making a mod that adds onto the code of a game and distributing that is incredibly different from distributing the code of the game. In a way, it's similar to how copyrights for translations are dealt with. For example, let's say that there is a novel written in, say, Spanish. The company that holds the copyright for that novel can either translate it themselves into English, or give the publishing rights to another company to publish it in English. Now, let's say there is are two companies given English publishing rights, one for EU and one for NA. Unless they get permission from each other, they can't use each other's exact translations, as each company holds a copyright to publish their own translations. This is partially why, in the case of anime and manga, it's considered a taboo to use a translation done by a scanlation team (one of the others being they're supposed to be higher quality, so why are they copying them).
Also, Mojang has already announced plans to implement a modding API sometime in the future, giving further implicit approval for people to mod their game, as there would be no point in adding such an API at all if people weren't allowed to use it.
The reason why Tekkit is looked down upon by so many people has to deal with the translation part of my example above. The publisher, Mojang, is giving implicit approval for other "companies," i.e. devs such as those for IC2 and Eloraam, to modify their code, as long as they don't distribute the core coding for the game. This gives the mod makers the publishing rights of their own mods which they can defer to other parties at will. With Tekkit, they don't get permission or, in some cases , are downright refused permission from the mod devs. To tie this in with the example, they're effectively publishing a translation of a work without the translator's permission.
