The water pump has now been replaced. I haven't heard the noise again.
If you read the forums (here and US) this sounds like a very common problem, but I haven't read of anyone actually have a FAILURE of the water pump - it has just been the annoying sqeeks (granted, that will probably lead to a future failure if left unattended long enough). That's why I reckon Jeep aren't doing a total recall, which would expensive. And to put it into context, although there seems to be heaps of people with these issues on the forums, more than 1 million JKs have been sold (with a reasonable proportion with the newer Pentastar), so perhaps the reported complaints aren't really a significant percentage.
But these problems make you tune right into every little squeek, rattle and bump... and send you bonkers looking for problems which aren't there.
You know, some people just drive their cars, without analysing every little thing to the finest detail. Those people enjoy their cars more. I wish I was more like that!