I don't think Francis Spufford (who wrote the article: also the author of
The Backroom Boys, which I believe has a chapter on Bell & Braben and
Elite;
Red Plenty, the only book of his I've read, which is an amazingly interesting and indeed exciting novelistic history of 1950s and 60s Soviet economics; and
Unapologetic, a defence of Christianity against Dawkins, Hitchens et al - Spufford is himself a Christian) is putting words or opinions into Banks's mouth. Iain Banks was pretty forthright about his views on religion, in his fiction and out of it too. The piece is more a summary, an analysis of how these views informed, in part, his science fiction, particularly the Culture novels. I don't know if Spufford knew Banks personally, but he is obviously a huge fan of his science fiction.
Iain Banks was an Honorary Associate of the National Secular Society and a Distinguished Supporter of the Humanist Society of Scotland. There's a short interview from BBC Radio where he speaks about his views on religion here, for example:
http://www.youtube.com/watch?v=6dnCTApJ4Bc
("Basically bananas", is the executive summary ...

)