Correct me if I'm wrong, but the Khitomer Accords would have superseded the Organian treaty. If it has dissolved, then the Organian Treaty is also moot.
The Khitomer Accords did supersede the Treaty of Organia, in 2239. this enforced the Organians' prediction that the Federation and the Klingon's would one day become allies.
P'Jem? Doesn't exist. Hasn't existed since the Andorians BLEW IT UP.
The Monastery of P'Jem was destroyed in 2151 by orbital bombardment by the Andorians, yes. The planet, whom some refer to as P'Jem also, is still there!
V'ger? Are you serious? Kirk solved that mystery in 2270. Mission complete.
After Dekker merged with V'ger, they disappeared, as they had transformed into a new level of existence. Who's to say that the Voyager/Dekker/Ilia lifeform cannot return to it's former reality for a visit?
First contact is a term used also for the first meeting of two species. Although first contact with vulcans occurred April 5, 2063, there was a first contact in 1957 in Carbon Creek, Pennsylvania.
There are thus two types of 'first contact'. But I also agree RR that a species joining the Federation would have to be approached and formal negotiations initiated. Perhaps just by meeting these aliens first gives the player the "right" to have this species on his side for gameplay purposes. This is probably what Cryptic is aiming at with this concept, imo.