That's an entirely different thing. Great Auks were hunted to extinction for profit, people liked buying eggs and stuffed birds for their collections. The reason might seem more scientific than hunting an animal for meat or bogus medicines, but it had nothing to do with real science.
The Great Auk was already well known and described by the time they were wiped out, and it was private collectors, not scientific institutions that pushed them over the edge.
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Obviously in some cases an animal is so rare that collecting specimens is a bad idea, but generally it's a good thing that we can compare modern animals to those for a hundred years ago or more.
If we didn't have collections of 19th century raptor eggs then we wouldn't have known about the disastrous effects of DDT, and we may have acted too late to save some species