Just a few comments. Software is a creative work, and hence as the author you hold copyright. As the copyright holder, you can license your work in as many ways you want, including releasing it to the public domain, which is what CC0 does, in contrast to licenses. (CC0 waives copyright, licenses assert it.)
First off, this is laudable! And putting a copyright-eligible work legally in the public domain should not be confused with expectations of professional norms to be followed, such as proper attribution and citation by those who use it, so you are not and need not be waiving that along with the copyright.
Second, if you continue to distribute your software primarily under GPL, you are within your rights, but you create confusion, for the reasons @mtholder is stating. So if you weren't ever planning to waive copyright, then doing so in one place but not in others is clearly not consistent with what you were trying to achieve.
Third, Dryad is not the only, and arguably (including for the reasons you mention) not the best repository for archiving software. Both Zenodo (http://zenodo.org) and Figshare (http://figshare.com) integrate well with Github in a way that allows you declare a release on your Github repository, which Zenodo or Figshare will then pick up, archive for perpetuity, and assign a DOI, which you can use for citation. And in this case you decide on the license, which presumably would be the license you have used for your code already. Here are two examples:
The latter of these is an archive of record for a paper now in press at Syst, Biology. The following is an archive of record for a pending manuscript submitted to MEE: