Murray, you absolutely cannot use the noise reduction system, or your timelapses will be extremely choppy. In fact, your intervals should not be longer than 7 or 8 seconds if you want to keep your night shots smooth.
If you need some advice or want to chat on the phone, PM me.
I would not be shooting JPEG either. I don't see how you could shoot 2500 frames per night if your exposures are 1 minute. I shoot 90s exposure night timelapses all the time and never fill up my 8GB card. Certainly not a 16GB card.
Here is a 1-minute sample of my night work to give you can idea of what can be done on a very simple 350D.....
http://www.timescapes.org/nightdemo720.movYou can achieve a great deal of noise reduction in the Camera RAW phase of processing the clips, in AE, for example.