First, sure it's okay to kill pvp flagged players. But when engaging the boss, we didnt have pvp flagged players in the raid. People got chain flagged because of bug abuse. I don't know who made this screenshot but it shows you my point: Several flagged horde players jumped into the boss and forceflagged melee. Then every single horde went into bloodrage and killed everyone and everything flagged, resulting in a wipe for our group.
Second, when you were engaging the boss, your whole raid was pvp flagged because of the bloodrage that happened. You went for the boss, knowing you can and will be attacked by alliance players. So it's okay for you to kill people who were forceflagged by bug abuse and griefing, but it's not okay to be killed when you KNOW that you are flagged and still go for the boss?
As you can see, alliance went for the boss and got forceflagged, which is apparently not allowed, and then killed.