Considering the Organians didn't want outsiders to interfere with their business (and probably gave the Federation a lecture of their Prime Directive) I'd think it would stand to reason that the peace treaty also included a prime directive for planets disputed by either two. How the Organians ensured that both sides would honor the treaty, is a different can of worms.
Considering the Organians didn't like outsiders, it seems likely the Organians had absolutely nothing to do with the Organian Peace Treaty. The two sides neutered by the Organians just made lemonade out of that particular lemon, and decided to agree on some things for a change.
Thus, when the treaty was broken, the Organians paid no attention. But the Feds would watch for Klingons breaking the treaty, and vice versa, in addition to doing their best to cover up their own violations. Until one side or both felt they no longer needed to cower behind a piece of paper, that is.
But if that was the case surely they would know where each planet in the Cetia Alpha system should be.
I don't see why that should be. Planets move, and Newtonian mechanics is a surprisingly inaccurate discipline when it comes to seven-or-more-body problems such as the Ceti A system. What Starfleet
would know is that the desert world in that system is Ceti A VI...
Command might have recieved preliminary damaged reports and decided the ship wasn't worth the effort of repairing.
But at the end of the movie, Kirk said the ship would continue serving. This either suggests he was in deep denial, or establishes that the "decommissioning" mentioned was of the top officers, not of the ship, and the decision to scrap the E-A came only later (or Kirk wasn't informed of it until later).
Yes, you are probably right. Did the ship have a science officer as far as we can tell or did he conveniently disappear?
None of the officers we saw wore the collar directly indicative of a Sciences job. We saw white on Capt Terrell, yellow on Cmdr Beach, green on a low-ranking female officer, and grey on Commanders Chekov and Kyle. Very high ranks there, compared with TOS... But Beach sat at the supposed Sciences station: perhaps he doubled as the ship's CSO, in addition to his "day job" (which may have been at Helm, since few other stations at the time accommodated yellowcollars).
Timo Saloniemi