I have yet to scrim this game, so take this for a grain of salt…
But personally I think you should leave them in. They really dont give you much to work with anyway, but leaving them in does add a bit more tactical strategy for the game. Do you rush the objective or do you risk being a man or two down to take the command centers or take them from the enemy? If you can take a few of them, it gives you a bit of a buff especially since you are taking away a buff from the other team. I think really the buffs will only hurt the worse teams than level you against a good team really.
The only reason it may be an issue is not really because they help, but because it may spread out the action in a 5v5 match. Taking this out of the equation, will force all teams to converge only on the objective. On the flip side there will be no other way to turn the tides of the battle (even if its a little bit).
So all in all, I dont th ink it hurts anything - but I wont care if they do or dont take it out.