One of the commenters to the article mentioned, money was never designed to be a tracking system. That "feature" has only been added over the past few decades.
And law enforcement will always be inconvenienced in a free society, the kind our founding fathers most definitely envisioned here in the U.S. (and elsewhere, I'm sure).
In this case, since Zerocoin is actually a university-sponsored project (from the Johns Hopkins Information Securuty Institute), we can hope for a response... hopefully it will be a rebuttal from the researchers and not a kneejerk response from administrators.
Even beyond its obvious utility (for good or ill), zerocoin is a fascinating problem in cryptographic research, and we should be grateful it's occuring in the light of day and not as some super-secret project.
[1] http://www.theguardian.com/commentisfree/2013/sep/10/nsa-mat...