To fix the issue of shooting clan members I've added the following friendly fire's plugin method: 

bool IsClanMember(BasePlayer player, BasePlayer possibleMember)
{
if (Clans == null || !Clans.IsLoaded)
return false;

var playerClan = Clans.Call<string>("GetClanOf", player);
var otherPlayerClan = Clans.Call<string>("GetClanOf", possibleMember);
if (String.IsNullOrEmpty(otherPlayerClan) || String.IsNullOrEmpty(playerClan))
{
return false;
}
return playerClan == otherPlayerClan;
}

and then added an "if" in onPlayerAttack: 
if(IsClanMember(attacker, target)) {
return;
}

It worked for me, but when this plugin update, I'll lose the configuration and will have to add it manually again. Did anyone found a better way to fix that?

You can easily create a plugin that utilizes the CanCombatBlock hook that this plugin provides along with the code you want.

Yeah, thanks for the tip Wulf, I guess I'll try to make a plugin for this! then I'll not have to worry about updating this one... :) If It works I'll post it here in umod... I searched for it but didn't found one that bypass this combat block when clan member...