Only read what you posted, not the longer article... I think that we should absolutely assess and evaluate the success of the program. The numbers on how many species are added, and how many are successfully removed, show that things aren't really working.
And the cross breeding example is an interesting one. To me that seems more like a symptom: the species is forced to cross breeding because the population is too low to sustain interbreeding. Killing off barred owls is probably the wrong move.
But that doesn't mean we should stop trying. Complaining about lost profits is such a slippery slope it's not even worth discussing, in my opinion. Once a species is gone, that's it, and no amount of profit can justify that.
So when a program doesn't work, we shouldn't say 'eh, survival of the fittest,' we should see what else we could do.
Post breaks rule 3