As mentioned by Robin in comment - http://bugs.koha-community.org/bugzilla3/show_bug.cgi?id=10942#c15 'They probably also should be going into /var, as writing to /usr is a bit of an odd thing to do really. This'll require more thought though.'
I possibly think that this ought to be superseded by whatever bug it is somewhere that has the translations being built as part of the package building process. This'd involve a lot of careful migration that would probably be better having effort put into doing it with the packages.
I think the bug you're referring to is bug 4861. I agree, this is a longer term piece of work which would be nice to get done.