If that's the case (and believe me, I've read Schachter's bit, and many of the zillions of "me too" posts following it, and so know the arguments inside and out at this point), I really don't have anything to say to you except "congratulations on your new job in the newspaper industry, I'm sure you'll fit right in".
I guess the main points were:
1) The shortener ought to be owned by the publisher; at least then the document and the identifier are connected within the same organization/entity/whatever. At least that way if the URL is lost, the document probably is too.
2) The shortening is necessary due to design decisions by twitter (and poor ones, at that.) Changing these in the right way could make the entire problem dissapear.
Punishing users is probably not the right way.
Now that's starting to change. By analogy: there's a legitimate use for DDT, and when I go camping once a year I happily buy a bottle of it, but that doesn't make spraying it out of a firehose around cities a good idea.
The person linking to your content is interested more than anything in bringing users to your content. If you put up a page that prevents them from doing that, then they'll use another link, or not link to you at all.
Really, it's about education and education comes at a cost. If you are educating, then you aren't focusing on coding or something else.
On the page where the javascript redirects, you could say, "Thank you very much for linking to my content. I think it's great that you appreciate what I have written, but please understand that the method you are using to link to it is not good and here's why: yada yada yada..."