I think the email goes further than poorly worded. It says pretty clearly that access will be cut off, gives no suggestion that there could be a negotiation.
I think it boils down to this, if the email said "Hey, we noticed you have special access, and we are trying to clean those up. You should either use the regular API with rate limits or our commercial offerings. Let me know if you have any questions." then I think the appropriate first step would be to contact Twitter and explain your situation. Since the actual letter contains that and just more information about possible options, I don't see why it should be viewed any differently.
> Hey, we noticed you have special access, and we are trying to clean those up. You should either use the regular API with rate limits or our commercial offerings. Your special access will be terminated on Thursday, April 21st. Let me know if you have any questions.
On receiving an e-mail of that nature, I would very likely let my audience know that I was shutting down the service on Thursday, April 21st just as the blog post author did.
I would not assume "Let me know if you have questions" meant "Let me know if you'd like to clarify your situation and request an exemption from this policy". I would assume it meant I could inquire about the details and process of the shutdown, or ask questions about the Gnip service or other options that they discussed in the e-mail.
Immediately going public can backfire, depending on the specifics of your case. Now there are possibly competing interests at play, the public pressure to let them continue, and possibly some anger over at Twitter for not being given the smallest benefit of a doubt (when their project works because of the good grace your company exhibited in the first place) or even asked before playing hardball. If I was the person responsible for making the call at Twitter, I would probably acquiesce, but I would want to tell this person to go get bent.
If they don't wish to communicate that message, the message should end with at the very least something like "We don't want to terminate a popular service in error, so please contact us today to tell us more about it."