Was the recent "conservation hunt" of a black rhino supported by science?
Yes it is.  Besides Dr. Knights article which is very focused on the issue and describes numerous benefits, there are other sources of research that show this can be good not only for the animals but also the community.  And specifically that this has worked in Namibia (where the black rhino was hunted) extremely well.

Namibia has encouraged communities to see their local animals as resources to be protected and that they can profit from.  In cases of endangered species, the federal goverment abides by CITES and only allows so many to be killed. Other than that limitation communities are allowed to profit from their local animals both from trophy hunts but also tourism.  This has led to a reintroduction of many of these animals (endangered and not) onto private lands.  The survival and thrival of these animals is now an economic concern to the communities and land holders, and are protected as such.  This has worked for the recovery of many animals in Namibia.  In summary, the selling of a license to hunt one black rhino brings big profits to the community and therefore encourage the people to protect these resources.

The CITES articles are also a good resource when looking at this.  It's very clear in the resolutions to allow quotas for endangered animals that it is not harming the population.

And one other paper, though it's behind a paywall, describes how South Africa's white rhino population went from fewer than 100 to over 11,000 as privatization and legal hunting were legalized.

As a side note, the wildlife conservation department where I live receives almost half its funding from hunting licenses.  Since it has been in operation the deer population has gone from nearly wiped out in the state to over half a million animals.

Flocken's arguments are based on fact but are really targeted at examples of bad wildlife management rather than against the practice of conservation hunting.  There is some concern that allowing the legal killing of any endangered animals will lead to more poaching, but I haven't seen any evidence in the literature of that.