They're going to view it that way no matter what. Whether someone says "I don't believe in God so I'm uncomfortable saying the Pledge of Allegiance" or "I would like the Pledge to go back to its original state", people are still going to think that they're un-American / "evil atheists" / persecuting Christians / whatever other bullshit you can think of.
I realize that. What I mean is that accusations will come to you no matter what you do. Point is,
just don't give them the reason to do so. They will still do so, but this will enable support from other members of the opposition who actually do think rationally and openly.
For instance, step into a rational Christian's shoe for once, and think who you'd most likely empathize and negotiate with: An Atheist who approaches respectfully for good negotiation, or one that rallies with a "Fuck Religion" attitude? Obviously the latter is looking for war, so the first thing the opposition will do is strengthen their guard.
The vast majority of Americans are Christian. We're in the minority. Most of them are going to think we're being disrespectful no matter our approach.
Ouch! I feel your pain there. Remember though; just because your enemy is being foolish doesn't mean you have to. The best method and image always triumphs.
Agreed, being a minority is harsh, but at this point you can't grab a flag and scream "Revolution!", because chances are you'll be crushed by the powerful majority. The methods I've seen work best at this point are usually political espionage or psychological warfare and manipulation.
There's a useful quote that Mr. Mafioso always uses:
"Keep your eyes open and your noses clean."