From the look of the noise artifacts, did you have noise reduction turned on? Noise reduction can sometimes make a noisy image worse, converting unobtrusive uniform noise into sharp artifact spots on a flat, noiseless background. If you had NR on, you might want to try a long exposure without NR to see if the noise is better.
Because of the amplifier glow (lower left corner of your picture) I'd guess you had NR off (based on experience with my own 1Ds3). I'd suggest turning it on. It's a pain but makes it mildly better. Still, this is not the ideal camera for astro work...
I don't know if any digital camera will give you a low noise 1 hour exposure.
There are some stacker applications used in astrophotography that will stack multiple shorter exposures to give you the same effect without the noise.
