John Horgan sends along this link to Anjana Ahuja's Science Notebook: I'm so sorry, you fellows, but I always religiously avoid your sort (this also contains a link to a piece by John that I linked to and commented on a while back).
There is one evident difference between the two cases: Ahuja did not accept the invitation and hence got no money.
It does seem reasonable for someone dogmatically opposed to the reconciliation of religion and science not to take money from an organization whose aim is preciselysuch reconciliation - though apparently it didn't bother Richard Dawkins, who was at the conference John attended and spoke in his usual uncompromising fashion.
It still seems to me that John and Ahuja are implying that scientists who are religious are intellectually dishonest. Indeed, if science and religion are incompatible and irreconcilable, that must be the case.
I also wonder if John would have had similar qualms, back in the day, about accepting funding from, say, the old Soviet Union, given that communism had in a relatively short time wreaked at least as much havoc as any religion has. In fact, the anti-religious ideologies of the 20th century were far worse than any religion. And religion gave us some good things - hospitals, manuscripts, glorious art, music, and literature. I don't recall any such benefits accruing from communism or fascism.