What challenges restrict the resolution of spacefaring digital cameras?

There is one overriding requirement for deep-space missions: reliability. In general NASA Preferred Parts are quite stodgy, because the overriding need is for a mature, well-understood technology. Cutting-edge technology that doesn't work is frowned upon under the circumstances. So 10-year-old image sensors are about what you expect.

Additionally, if you read the JunoCam article you linked, you'll see (second paragraph, first sentence) that data transfer rates are quite slow, on the order of 40 MB per 11 days. Increasing image size cuts down the number of images which can be acquired, and I expect that a lot of effort went into determining the tradeoff between number of images and image resolution.

For what it's worth, NASA has been pushing for better data rates for its programs, but the limited power and long ranges involved make this a non-trivial problem. The LADEE mission a couple of years ago incorporated the LLCD (Lunar Laser Communication Demonstrator) which worked quite well, and this holds great promise (optical communication limit of 1 bit/photon at the receiver), so future missions may be able to do a lot better.

You seem to be under the impression that the quality of photos taken in space is limited by the sensor resolution, which is not the case. Equally important factors are the sensor sensitivity, which gets worse as you increase the pixel count, and the robustness of the optical system.

Simply put, if you were to send a 10MP DLSRs camera on Jupiter, it wouldn't be able to focus properly (or at all) after the vibrations it experienced during launch to the point where the actual sensor resolution wouldn't matter. Plus, it wouldn't get enough light to make quality photos.

Think more like 10 years before launch. Once it's designed, it's designed - changing components is a major risk factor and they're unlikely to want to do that. A massive amount of that time will have been spent on testing.

This is the appeal of small, semi-disposable satellites with cheap launchers going into Earth orbit - if you lose one then it isn't such a big deal. With massive investment in money and time getting this thing to Jupiter though, adding risk is generally Not A Good Thing.