Coobeastie and Eddie, I've heard those reasons given, and also the one that says they're afraid of thieves photographing things they want to nick. I'm not sure how far they hold water. The National Trust has for years banned indoor photography; but they did a survey of members a couple of years ago - I was one of the ones they phoned up and I made the point strongly that I was not renewing my membership, because I was fed up with being treated as a thief by an organisation I'd paid to join. Interestingly, this year they've rescinded the ban (it still exists in individual properties, sometimes where precious objects aren't owned by the NT itself.) For the sake of tapestries and so forth, flashes are still banned. I don't really think light is a problem in St Paul's, though; it's a cathedral, not an art gallery.
As for the buy-the-guidebook rationale, they could get round this, as many places abroad do, by charging extra for photo permits, so that if you didn't buy the book they'd still get money out of you. I'd find that acceptable; I don't mind paying to exercise my hobbies.