I have a few points to make here. First of all, you might think that GCHQ would be intolerant, but they are actually more concerned with people being vulnerable to blackmail and, of course, once they know about your record, it probably makes you a lot less vulnerable to blackmail. For most types of offence.
Whether or not it is indirect sexual discrimination is an interesting question, and good luck with getting anyone official to take it up. These days, despite all the government's assurances and empty promises and aspirations, nobody wants to be seen to be "soft on criminals". You could try the Equality and Human Rights Commission, but even if it was declared unlawful to have a blanket exclusion, those employers who wanted to get round it could do so quite easily by using a different excuse, unfortunately.
I'm not sure how sexual discrimination became sexual offending, even though I'm sure the vast majority of people on the SOR are men. Maybe we should call it gender discrimination instead.
As Chris Stacey said: Although its not formally part of the sentence that is handed down in court, the criminal record that someone comes away with effectively becomes a second sentence, which can have a long-lasting, if not lifelong, impact.