What are the good reasons for shying away from religious conflict? One is division of labor. There are endless weird claims of the paranormal and supernatural that are begging for the application of critical thinking, from astrology to dowsing to ESP to ghosts to telekinesis to zero point energy, and while religion is a gigantic sinkhole of ignorance and absurdity, there are atheist organizations that deal specifically with that subset of human folly — it's entirely reasonable that a skeptics' group might decide to distinguish themselves from atheists' groups by focusing on a different set of phenomena. The James Randi Educational Foundation and the Richard Dawkins Foundation for Reason and Science are and ought to be differentiable. We've all also got limited time; I think tarot cards are complete bunk, but I haven't spent any effort on ripping them up, just because I've got other targets I find more interesting. We need many people and many organizations to address the whole wide ecosystem of kookdom, and they can't all do all of them.
Another good reason is operational: skeptical organizations tend to work on existing phenomena and individuals, with little effort spent on vague historical claims. They will argue that many psychic and supernatural claims are little more than cheap magic tricks, and they will track down and expose charlatans who are bilking people right now with claims about spoon-bending or talking to the dead; there are so many of those at work right now, that showing that some weird Jewish rabbi living 2000 years ago was just doing trivial sleight-of-hand and psychological manipulation is both less interesting and less directly testable, even if the skeptics are pretty darned sure Jesus was a con man. Nebulous assertions that Jesus loves us are untestable and uninvestigable, but you'll notice that if there is specific claim of a weeping madonna statue, skeptic Joe Nickell isn't shy about demolishing it.
These are eminently reasonable rationales for not pressuring skeptical organizations to join ranks with and become inseparable from atheist groups. There is also at least one awful reason I sometimes hear: that skeptics should avoid criticizing religion because it might alienate some of their fellow travelers. That's unconscionable, and implies that they aren't really interested in critical thinking, but in simply growing an organization without regard to its purpose..."
"So those are our alternatives: demand perfect purity from all skeptics, or shut up about the foolishness of religious belief. Neither are going to happen. I'm particularly disgusted and amused by the claim that it would be "more respectful to present ourselves honestly and openly" while demanding that we stop mocking the absurdities of religion."
"Go ahead, go to church, believe whatever you want. But you don't get to whimper that skeptics and scientists aren't allowed to disagree with you simply because it is your belief. Faith is not a get-out-of-jail-free card. It's an affliction to be overcome."