Motors create all sorts of nasty noise, replacement motors really shouldn't have that much of an effect in that regard. In any case it's unlikely to be the motors and more likely to be the controller board drawing down loads of current every time the motor makes a step. The trick is stopping the noise affecting other devices.
One thing to check would be the performance of your 12V powersupply itself. Try running the thing of a brand new 12V battery and see if you still have issues. Poor output regulation of powersupplies can cause other loads which suddenly draw current (like steppers) to create voltage dips for all the other devices to enjoy.
If the noise is high frequency then ferrite beads which clip on to the power lead like this
http://forum.flitetest.com/attachmen...2&d=1361046410 may be the answer. Not sure about your mount but the 12V power cable for my mount and the power cable for my battery both came with those clip on beads already.
Then there's a possibility that the camera itself has had a regulator fail which is passing voltage to the output. Not much you can do about that one other than send it back unfortunately. Know anyone with an EQ6 you can try the camera on?