Yes, they do want genetic diversity when they breed animals in captivity, so that reintroduced populations are better able to survive. That is what the stud books are for, not to keep "pure" and inbreed, which loses the genetic characteristics which make strong flexible groups.
But they do not want populations which have completely separated to merge and lose their characteristics.
Take zebras. You would probably think a zebra is a zebra is a zebra, most useful as the last animal in an alphabet book.
But there are three species of zebras: the plains zebra, the Grévy's zebra and the mountain zebra. The plains zebra and the mountain zebra belong to the subgenus Hippotigris, but Grévy's zebra is the sole species of subgenus Dolichohippus . The latter resembles an ass, to which it is closely related, while the former two are more horse-like. All three belong to the genus Equus along with other living equids, but their lifestyles differ.
Like most members of the horse family, zebras are highly social. Their social structure, however, depends on the species. Mountain zebras and plains zebras live in groups, known as 'harems', consisting of one stallion with up to six mares and their foals. Bachelor males either live alone or with groups of other bachelors until they are old enough to challenge a breeding stallion. When attacked by packs of hyenas or wild dogs a zebra group will huddle together with the foals in the middle while the stallion tries to ward them off.
Unlike the other zebra species, Grevy's zebras do not have permanent social bonds. A group of these zebras rarely stays together for more than a few months. The foals stay with their mothers, while adult males live alone. Like the other two zebra species, bachelor male zebras will organize in groups. Plains and mountain zebra foals are protected by their mothers, as well as the head stallion and the other mares in their group. Grevy's zebra foals have only their mother as a regular protector, since Grevy's zebra groups often disband after a few months.
When they are promiscuously interbred in captivity, the offspring are not representative of their original populations, so are able neither to fit in if released nor to serve as examples if kept.
(A lot of this description of zebras came from Wikipedia - must remember to quote sources
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