[Gothmog]

I agree with Rune here, the ents and eagles was probably sent to ME for a reason and they had their mission, but within the limts set up for them they were free to act in the way they thought was most suiting for the moment.

But how does the creation of species work? We know the elves and men were created by Eru and that he gave them a "free will" or whatever you want to call it. But when Aule tried to create his own people they became creatures without a real soul. Eru tells Aule this:

Why hast thou done this? Why dost thou attempt a thing which thou knowest is beyond thou thy power and thy authority? For thou hast from me as a gift thy own being only, and no more; and therefore the creatures of thy hand and mind can live only by that being, moving when thou thinkest to move them, and if thy thought is elsewhere, standing idle. Is that thy desire?

Apparently the Valar can't create anything with it's own will. The dwarves were blessed by Eru in compassion so they became a free people.

So if the ents and eagles were created by Valar, they would not be able to act other than on their command. But now it's Eru that tells Manwe about the spirits that will inhabit certain Olvar and Kelvar. Sure, it was in Yavanna's and Manwe's thoughts in the Song, but it was Eru that finally made it happen, gave the Ents and Eagles their "souls". Here's the section (Manwe to Kementari regarding what Eru has told him):

Do then any of the Valar suppose that I did not hear all the Song, even the least sound of the least voice? Behold! When the Children awake, then the thought of Yavanna will awake also, and it will summon spirits from afar, and they will go among the kelvar and the olvar, and some will dwell therein, and be held in reverence, and their just anger shall be feared. For a time: while the Firstborn are in their power, and while the Secondborn are young. (emphasis mine)

I think that proves that the guardians of kelvar and olvar wasn't something Yavanna or even Manwe created, other than perhaps their physical shape. The spirits was, if I understand this correct, put in them by Iluvatar. Therefore: Ents=free Eagles=free

But what was these spirits? Spirits of ME or from somewhere outside the creation? That's an other discussion...