I work at an FFRDC similar to the JPL. Granted the work that is done at the FFRDC that I work at is more defense related, so the argument is a bit different, but I honestly don't see the big deal. Is some of it a bit extreme? Sure. I don't think sexual orientation should come into it, but I can certainly see financial background checks. There are certain flags that make someone susceptible to espionage, whether corporate or governmental. One of those things is financial need.
In beginning work at the FFRDC, I was made fully aware that my background was going to be fully investigated as a part of my job. In having a security clearance, I wouldn't want it any other way. There is also NO assumption of any privacy while on the FFRDC (or adjoining Air Force Base's) grounds including when things are encrypted in transit.
I think I saw the argument made that a good deal of their information is not classified. This doesn't mean, however, that if the information were released to the public, or to another organization, that it wouldn't hurt the JPL. FFRDCs compete between each other for customers, often HUGE customers like Boeing, Lockheed Martin, General Dynamics and other large defense contractors. Losing information in an industrial espionage-type case to another FFRDC could mean the loss of millions in dollars in sponsorship money.
The bottom line here is that the JPL, while less defense oriented and more research/exploration oriented, is still an FFRDC and is aligned with the DoD in some manner. The government has a responsibility to ensure that the information that it and its sponsored organizations work with is secure and the people who generate, work with and disseminate it do so in a responsible manner.
If for some reason the DoD or my employer finds it necessary to increase or modify the checks that it is doing on me, that's fine. I'm usually made aware of this. If not, that's fine too (to me). I understand the nature of my work requires it and if at some point I don't like it, the option is there to leave and work elsewhere. I'm no indentured servant.
People often forget (including people that I work with who have been there for many many years) that they're not just there for a purely scientific goal; They're there to apply technology and research to the national security of their country.