Its a good idea but you need some finesse here. Extending the wires from the CCD means there will be more electrical noise induced in them, whether it be more voltage drop or induced capacitance hum from surrounds or your body etc.
Maybe you should use twisted pair wires or coaxial wires. I'm in favour of twisted pair for clean signals but in this case because of the signal type I'd go coaxial cable with the shield well earthed.
Maybe even ensuring that it does earth thru a earth stake to dump all EMI.
Also at this stage have you thought about the CCD power supply. I would suspect the one on the cct is cheap and not regulated much (probably its fed by a power pack). Could be a good time to build in a good low ripple supply for the CCD and cctry ....maybe even battery for the CCT and cctry.
Good work, keep it up. I'm dying to see the results.
edit:
forgot to mention, beware moisture build up from the peltier onto the CCD.