The secular side only has to win "eventually" in order for it to argue against Stross' point. In any case, even in the case of abortion, which triggers powerful disgust reflexes, there isn't anything like a holy war against abortion, let alone a holy war with a good chance of succeeding everywhere in the world.
http://en.wikipedia.org/wiki/Anti-abortion_violence
I do agree that the "holy war to end holy wars" phrase was hyperbolic, but it's also hyperbolic to expect no objection from religious people. When Stross first addresses the issue, he says:
...However, if it becomes plausible in the near future we can expect extensive theological arguments over it. If you thought the abortion debate was heated, wait until you have people trying to become immortal via the wire. Uploading implicitly refutes the doctrine of the existence of an immortal soul, and there
I periodically get email from folks who, having read "Accelerando", assume I am some kind of fire-breathing extropian zealot who believes in the imminence of the singularity, the uploading of the libertarians, and the rapture of the nerds. I find this mildly distressing, and so I think it's time to set the record straight and say what I really think.
Short version: Santa Claus doesn't exist.
- Charles Stross, Three arguments against the singularity, 2011-06-22
EDITED TO ADD: don't get your hopes up, this is pretty weak stuff.