There is a similar whale shark research programme here in Taiwan, in Hualien, where they study the animals for a short period before releasing them or passing them on to other research establishments. I believe the last animal was transported to the States. The animals are kept in very large skein nets moored offshore and, typically, they are released prior to the arrival of any severe weather (we get a LOT of typhoons) so that there is no risk of entanglement if the net sinks. The same facility runs similar research programmes with manta and mola mola.
The research facility here in Taiwan helps to fund itself by offering small groups of divers the chance to enter the net, on scuba or free-diving, with the shark. From what I have seen in the media the operation is humane and mindful of the welfare and the needs of the animals in their care.
Whilst I have not dived the nets, I know that Taiwan is a country which needs all the education on whale sharks, and indeed sharks generally, that it can get. Su'ao, Taiwan (and probably elsewhere) has a shark fishery and has been known to take whale sharks and the demand for sharkfin soup remains fairly high in the country, though educational programmes may yet yield some success. If more people in the traditional markets for shark and sharkfin can be shown how endangered these species are, and how unsustainable their consumption is, then perhaps we will have a better chance to save them.