Since I am about to commit to using my North Ithilien Essence Boxes, which means I have to choose which essence to take, I tried to track down rumors about the possibility of upgrading them in the future. As they are now, the teal Ithilien Essence of Morale beats the T8 Supreme Essence of Morale, but the other teal Ithilien essences are not better than the corresponding craftable Supremes. Since I need more morale essences than any other (and it has the most demand on AH), that seems like a safe way to go.
I found a youtube video from the Update 19.1 beta that showed more details of the possible scheme for upgrading the Ithilien essences. See starting at 2:54 and 7:50 for interesting details.
www.youtube.com/watch?v=7quCLCwwVVs
Note that Update 19.1 went live without the upgrade feature in it (we're currently on 19.1.1), but it suggests that they will be upgradeable eventually. Details may change, but it shows how the devs are thinking about it. One important thing to note is that the upgrade process is more like crafted relics, in that you craft an item that you barter, rather than crafting the new essence directly. You barter it for an Ithilien Infused Essence Box, which presumably lets you select whichever essence you want. This would mean that if I extract an Ithilien Essence of Morale now, I could later "upgrade" it to be an Ithilien Infused Essence of Agility (or whatever the choices turn out to be) as well as the upgraded Morale.
Of course, since this was beta, things may end up different whenever it goes live, but it suggests that I don't have to worry about regretting which essence I select now when the upgrades are available.