Trust me, as a guy who has seen every single LA Galaxy game since 2003 I can assure you they have the ability to remove the lines. Maybe they don't for a NE vs Columbus match but they most certainly do when Beckham and Donovan come to town for a national game.
A quick check shows since Beckham has been with the Galaxy they have never played in NE during the NFL season--pre-season but never during the regular season.
I have family in Boston who go to Revolution games and they say the same thing, it is tough to watch the games with the football lines and rightfully so, the Patriots are priority #1. They can't ever remember the lines being removed for an MLS game once the regular season kicks off.
This is a silly argument anyway. MLS will always have a neutral site for MLS Cup and they will expand the playoff format. The only chance of change happening is getting rid of the geographic divisions.
I am just glad they are bringing back the reserve division, that at least is a step in the right direction.
I still hate that a US league will now have multiple Canadian teams in it and the southeast US is completely unrepresented.