The chapter on the Hexagram ritual in Pearls Of Wisdom also has an alternative Analysis Of The Key Word created by James Eshelman which replaces the old aeon elements with a Thelemic one.
All due respect to Lon DuQuette - I love many of his books and have had the pleasure of attending excellent workshops and lectures by him - but his Magick Of Thelema book contains same versions of the Pentagram and Hexagram rituals that one will generally find in print elsewhere which are little more than the Liber O "crib notes" which lack a certain amount of explanation on some details. Namely, in the case of the Hexagram ritual, the macrocosmic elemental attributions and the use of the notariqon / acronym ARARITA (as with AGLA in the case of the Pentagram ritual). I still think it's a book worth reading, but do so along with Pearls Of Wisdom. Also I highly recommend experimenting with these different versions of the rituals and seeing what works best for you.
Regarding Thelemic versions of the Pentagram and Hexagram rituals (also Middle Pillar rituals) which have been developed by different individuals and groups, the Analysis Of The Key Word in the Hexagram ritual is about the only thing in any of these rituals which can be called "old aeon" and could be at all considered by any stretch "un-Thelemic". Even then, I think that would be a little a bit over the top to say. It still has value for the Thelemic practitioner up to a certain point. James explains it, and alternative options, in the relevant chapter of Pearls Of Wisdom. In most circumstances, and especially for one early in the path of their magical practice, the use of the classic Analysis Of The Key Word isn't going to be of any hindrance to the efficacy of the Hexagram ritual. But again, read up, and experiment, and see what works for you.
As for everything else in the Hexagram ritual, Pentagram rituals, and Middle Pillar ritual, there is nothing un-Thelemic about anything to do with them. Indeed, generally all that's need to transform the standard Pentagram ritual into a Thelemic Pentagram ritual is the vibration of Aiwass at the heart centre during the opening and closing Qabalistic Cross. I've seen many, many new versions of Pentagram, Hexagram and Middle Pillar rituals - especially online - which replace the Hebrew words and names with those from the Thelemic pantheon, and while these are interesting to read, one could take away the very mistaken belief that the Hebrew Qabalistic god-names are somehow antithetical to Thelema and to be avoided. Pretty much all of Crowley's ceremonial magical work, and the ceremonial magical methods and tools he taught, are based on Hermetic Qabalah.
I understand that some Thelemites see YHVH in a ritual outline and are concerned by connotation that it's Judeo-christian / old aeon and therefore un-Thelemic. However, that point of view is - imho - mistaken since the formula of YHVH appears throughout some of the most Thelemic of texts and rituals. Also, if an individual Thelemite magician is so hung up on being opposed to Judeo-christianity then that resistance / reactiveness will have to be confronted and worked through at some point in their path (just as the potential reactiveness of one from a christian background will encounter within Thelema when confronted with the use of archetypes, ideas and names of Satan, Beast 666, Baphomet etc... it works both ways).
I'm aware of some Thelemic groups who practice the Star Ruby in place of traditional banishing Pentagram rituals and Reguli in place of traditonal invoking Pentagram rituals. That's fine, no problem with that, but I would argue that the Star Ruby is somewhat different in effect from the Lesser Banishing Ritual of the Pentagram, and that Reguli is considerably different in effect from the Invoking Ritual of the Pentagram. Once again, only the individual's own experimentation and prolonged work with these rituals will reveal what is best for them.
Finally, a point to consider on this topic, if the Pentagram and Hexagram rituals were un-Thelemic, why would Crowley still continue to use, teach and recommend them long after he received and accepted the Law of Thelema? To my knowledge (looking at the editorial notes in Liber ABA / Book 4) he was still recommending the use of the Pentagram ritual in the 1940's, long after he had created the Star Ruby.