If they had so much time, then they did a very bad job by coming up with such a thin and unconvincing story. If we watch the season 3 episodes including "Scorpion1" and then "Scorpion2" and "The Gift" we can see that there are some good episodes with Kes as a main character with much importance, such as "The Swarm", "Warlord", "Darkling", "Before And After" and "Scorpion1" where Kes gets a lot of action. Not to mention that "Year Of Hell" was originally supposed to be the cliffhanger between seasons 3 and 4 and also a follow-up to "Before And After". Clear indications that Kes was becoming an important character. On the other hand, we can see Harry being more and more shoved aside with only one episode where he had a prominent role, "Favorite Son". In "Scorpion 1", Harry is close to death and it was easy to assume that he would be killed off during "Scorpion2". But suddenly Harry recovers in a miraculous way and then we have the patchwork story in "The Gift" and all of a sudden, Kes is gone instead. So whatever the writers were doing during the auditions for who would become Seven, it don't look like that they were planning a goodbye story for Kes, more that they were planning Harry's exit, if they were planning anything at all.