This is interesting.. You choose real wars as a example, this is "Star Wars" not real life.
now even in real life the factions have talked between troop wise. in the civil war they did it all the time.
That being said faction is just alignment that should not affect anything you can make friends in both places.
If you want a great example of what I am implying Star Wars Galaxies is a perfect example for this, the game lasted 8 years, that's a long time for those who cannot see the big picture.
In regards to the harassment that's what ignore is for..