In case that the forked software project adds enough novelty to be considered a research product on its own, it should be alright to just list all the contributors to the fork and not those to the original project.
Citing the "Software citation principles" article (Smith AM, Katz DS, Niemeyer KE, FORCE11 Software Citation Working Group. (2016) Software citation principles. PeerJ Computer Science 2:e86 https://doi.org/10.7717/peerj-cs.86), section about derived software:
In the case of one code that is derived from another code, citing the derived software may appear to not credit those responsible for the original software, nor recognize its role in the work that used the derived software. However, this is really analogous to how any research builds on other research, where each research product just cites those products that it directly builds on, not those that it indirectly builds on.
Transferring this principle to the question at hand the way to go is removing the contributors to the original project from the list of contributors for the fork. The new version of Zenodo released last week (Sep 12, 2016, https://www.openaire.eu/zenodo-relaunch) features improved GitHub integration. So it is now possible to adjust the list of contributors.
Any other opinions are welcome.