You say that, but you disregard that GCHQ invented RSA public-key encryption. Of course, nobody knew that they did, because it remained top-secret classified until 1998, 20 years after its public release by a set of people who created it independently (hence the naming). Who is to say just how other many inventions/discoveries remain top secret for a few decades to come?
Lets also not forget that Alan Turing worked for GCHQ cracking the German Enigma code.
Yes there will always be the work happening in academia, but to claim that a lot of "interesting work won't be done at GCHQ" strikes me as disingenuous, with little more to support that than mere supposition. One cannot know either way, but history tells us that interesting work in security was indeed occurring at GCHQ, and so the more reasonable assumption to make would be that the opposite of what you claim is true.
The idea that just because firm x pays zk less than firm y is a "rip off" is rather silly. It does suggest one is motivated only by money. There are many other factors to a job that simply cannot be quantified with an equivalence to the pay. My friend who has recently completed his PhD has gone to work at an investment bank, and told me he was being paid £36k. Gobsmacked, I said I'd have expected it to been £15k higher, given he had worked there previously and as an intern during his PhD. He told me that he had taken the option for lots of additional training, all paid for by the company (and not coming out of his own wallet). A smaller pay check keeps him in the lower tax band, and the company pays for the training, rather than him. His pay looks smaller but is in fact larger. On the other hand, his girlfriend, also working in finance, and for less, is in an office where she regularly stays in work later than 7PM, and is getting paid less for it. Could one have inferred that from the salaries alone? No, in fact one might have assumed the other way round.
Before I started my PhD, I worked at an IT company paying £26,000, and within 2 years I had upped to £30,000, with a prospective £35,000 on the table if I had not left to do my PhD. Again, something you cannot infer from the advertised salary, is the rate of progression. We also had a pool table at work (which I spent significant amounts of time at). If I'd gone to a bank to work for £35,000 starting salary, who is to say my progression would have been the same(or similar), that I would have had a pool table I could visit whenever I liked, that I would have even enjoyed the job as much as I did. Would I have been able to clock off exactly once my hours were done, as I did at my previous job? Would I have been in a silent room full of people glued to their desks, or would it have been vibrant and full of lively discussion, like my previous workplace? Truth is, one does not know if the advertised salary represents value for money until they actually do the job.
Not having mentioned cost of living yet, the job at GCHQ could represent excellent value for money, particularly in terms if training, flexibility and workplace ethic, all things which are hard(impossible) to guage from the job advertisement. To judge it as underpaid or a rip off, well, you can't unless you've worked in those roles.