Yes, but are assists rewarded?
Yes. You get an award for the most assists.
I've also noticed that, because I am usually the only one on my team who locks strategically important flags, and because I keep running around locking them, I usually end up with the least kills and least experience, and thus, the least favor points.
There's an award for the most flags capped as well. Naturally you're going to have less experience and kills if you spend the majority of your time flag capping. Balance your priorities, and cap flags after you kill the enemy.
Yet, I'm fairly certain that in a few of those games, if I did not lock the flags as often as I did, we would not have won.
Probably true.
Imo, this game rewards you for the killing of another player far too much, when really, the game is won by holding flags and upgrading the citadel.
There is an award for citadel upgrades as well. If you spend most of your time killing people you'll probably get the kills, kill streak and gold awards. If you play as the way you described you'll probably get the citadel upgrade, flag and assist awards. In reality you'd get more favor, since the gold award is only worth 10 favor while the others are worth 15.