This thing really is a can of worms, in terms of: 1) The impact on the ecosystem if characters are counted after link wrapping. 2) The impact on Twitter's core system and SMS communication if characters are counted before link wrapping. 3) The perception that there is no guaranteed stability in the TOS, which makes developing and investing in the ecosystem increasingly unattractive.
I don't buy the click tracking privacy argument. Twitter will have no more insight into clicks than what bit.ly or any other shortening service has, and they won't have any insight into clicks on links that are not in tweets. For example, if I tweet something with a bit.ly link and I use that same bit.ly link in other places, Twitter will track only the clicks on the link in the tweet. They are not able to track the clicks on that bit.ly link in the other places I've used it (Facebook, Buzz, StatusNet, blog, etc.). If the privacy argument carried any water, then bit.ly would be a far greater privacy threat than Twitter.