Biosystematics is just complicated
The problem with saying "Biodiversity for the sake of Biodiversity" is misguided, as to not understand the scope of the problem.
In a nutshell, the problem is that biodiversity is just such a complex thing, and that in many places not that fully documented, especially at the smaller end of the scale (South Pacific Coleoptera, Nematoda for example) is that we simple don't know what's important. If we don't know what's there, we can't know what's important, so it's easier to just protect everything while it's being investigated (which given the time scales in Biosystematics might take centuries.
Dominic