Actually it isn't an issue with pets or totems. It's more an issue with the radius it hits. If a player is in range to be hit by it, which is a very generous range of like 8-12 yards, then it bounces off the player instead of hitting the boss. More likely the issue you are having is simply that players in melee aren't moving enough out of the way so that it is a clean hit on the boss alone.
I raided and killed this guy on an alt with two hunters last night who had their pets on the bosses back the entire time which was in the path of the orb. Additionally, all of the totems from the one Restoration Shaman were also between the boss and the ranged group right behind the boss.
You're overcompensating and assigning blame incorrectly. What is probably happening is your people simply got better at moving out of the way and it just started coming together for you. It had nothing to do with the position of the pets or the totems.
"In anything, if you want to go from just a beginner to a pro, you need a montage." /w TankSpot WTB Montage for Raiders.