Treebeard's words are also addressed in Letter 153. There Tolkien says:
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Treebeard does not say that the Dark Lord 'created' Trolls and Orcs. He says he 'made' them in counterfeit of certain creatures pre-existing. There is, to me, a wide gulf between the two statements...
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Tolkien then proceeds with the 'rational incarnate' statement which I quoted above. Also keep in mind that while Treebeard was immensely old, he was not one of the 'wise'; i.e. not one of the Ainur privy to at least some portion of the truths concerning Tolkien's sub-created world. Thus his beliefs and indeed those of the Elves remaining in Middle Earth (who were uninformed of the Valar's views of Orcish origin - it is not clear that the Valar encountered Orcs before the First Age) are not necessarily the whole 'truth'.
The difficulty arising from the Morgoth's Ring materials is that they were often ideas in flux. Thus there are multiple views concerning Orcish origin. However, Tolkien does not seem to waver from his view that they arose in whole or in part from sentient Elves/Men who possessed Feär. This seems ratified by Tolkien's statement that Orcs would proceed to Mandos upon death. If they lacked Feär, there would be no need for this.