It comes with being on the site for a while, and with actively writing. It comes with character's goals too, no matter how time and concrete conditions might twist them. 

After a while, characters can switch factions, and it is all right.  

It took a while for me to understand that it is all right, but now (and for a while, not only now) I understand it. In the first two years of roleplaying, I didn't understand it because I was thinking only at the freshly reopened slot in the initial faction, seeing it as a sort of betrayal to the faction. And when one of my characters had to change factions, I said that it was OK only because I had another character in that faction, so the faction wouldn't remain deprieved of one character.

Now that somebody wants to change factions... it makes sense for the character. I know it is a good character development. I know that the faction he is leaving would manage without him... We'll be all right. He might be all right as a civilian on an island too, starting a new life. And maybe it is interesting to explore this side of the story as well. 

Still I feel sad and a bit betrayed, even if I know I shouldn't.  I resent his departure from the faction, and I am as sad for his leaving as his captain and crewmates would be, in the story, when hearing about it. And this, because the writer has only one character and no intention to make more. Something will be enriched, with the price of tipping down the other scale of the balance, And this feels sad. But it is a sadness which will pass  The story goes on, and it will be equally interesting. Characters do evolve and change paths in their story life...