Heh, I can't believe this is still raging, and so many people still refuse to read more than the incendiary headline.
Pratchett is not demanding every future Dr Who script is fact checked by NASA, he's saying that although he really LIKES the current Dr Who show (please read that part again), he thinks that sometimes the plot resolutions can be somewhat weak and reliant on 'magic fixes', instead of something clever, or something returning from earlier in the show to save the day.
He's not saying it's bad, which is why 'attacks' is a godawful word to use in the headline, he's just saying that if he had the choice, he'd prefer that one element to be changed for the better, he also understands that it's good fun entertainment, and shouldn't be analysed too deeply.
As for Pratchett not following logic and science himself, his 'discworld' runs on its own logic, based fairly heavily on tropes and the stereotypes of fantasy, and while that's not suitable for everyone, he generally sticks to his own set of rules, once they're set up.
As for the 'crazy idea of golems following information written on a piece of paper inside their heads' that's a nod to Asimov's rules of robotics, respected sci fi. So much of his writing is related to things in our world, such as the idea that magic is designed to not be used, not by people who can't use it, because that's easy, the hard part is not using magic when you can. That's essentially based on international nuclear weapons stockpiling to my mind.
"We've got all this power and we could use it, but I know you can use it too, so lets just not, ok? Especially as the last time two wizards duelled in a city, that city ended up a glowing swamp with sentient frogs living in it."
On a side note, it sure got people talking, anyone else want to post something mildly critical from one fanbase to another? *hides*