Funny thing is, they could've easily moved on from Spock after WoK by having Saavik replace his archetype and have David fit into McCoy's (if they wanted to remove McCoy as well).
Then we'd still have the Freud archetypes that drove the trio's interactions, but the dynamics would be affected in that the Id was Kirk's son and the Superego was a female who may or may not have gotten romantically attracted to the Id.
But that would've just made Trek a bit soap opera-ish...
I'm so glad you're keeping the idea of the archetypes alive.
They are Jungian, not Freudian, though, and the id, ego, and super are "parts" of our psyche as Freud envisioned. The id is the basic, animal survival urges. I don't think someone on TOS stood for those other than id-kirk in "Enemy Within." And superego is one's conscience internalized from one's culture, though there seem to be some cross-cultural universals. MAYbe McCoy, sometimes, arguing from ethics over Spock's rationality. Sometimes Spock, though.
I see them more as reason (Spock) and passion (McCoy) mediated through the whole-man hero, Kirk. You might be on to something with Saavik taking the place of McCoy for passion, as there is an archetype of the spunky, chaotic good female who is passion/nature. Princess Leia fits that role. Fun discussion.