Normally, without Precise Shot, firing into melee through an ally at an enemy would result in a +4 AC for the enemy (Soft Cover bonus) and -4 to attack roll (firing into melee).
Precise shot negates the -4 modifier.
The Friendly Fire teamwork feat says:
You initiate this feat as a standard action, making a ranged attack against a foe engaged in melee with at least one abettor. This shot deliberately forsakes normal precautions, putting your abettor at risk, but also is unexpected enough to surprise your mutual opponent.
You gain a +2 bonus on your attack roll if the attack passes through an abettor's space. If your shot misses the target, you must immediately make a second attack roll with all the same modifiers against the abettor, potentially hitting her with the attack instead of the opponent. When the attack resolves (regardless of whether either potential target was hit), the intended target's startled reaction provokes an attack of opportunity from the abettor.
So now we're looking at a +2 for the attack roll. Is the soft cover now negated by the sentence at the beginning of the second paragraph? How does this end up working out? My gut says the soft cover still applies a +4 to AC, but the attacker still gets a +2 to attack.
Your gut is correct.