All Stack Exchange sites, including meta sites, run off a very similar code base. Because they're running basically the same code, meta sites like this one get the same list of badges. Removing them would potentially mean moving the meta sites to a separate code base, making the changes to remove them, then maintaining two code bases in the future.
Even if they went about it in a more maintainable way (config parameters to turn them on and off, for instance), they still would have to put in all the work to do that in the first place. And as it stands, the badges aren't really hurting anything. And there are only a handful such badges, anyway (I think there's something like eight). In fact, the ones for earning rep are still possible; we have thirteen Mortarboards here.
So basically, there's virtually no benefit, and potentially a lot of headache. It's not impossible, but it's very unlikely to ever get done.