Well, I am no expert in ICE... But you know , Fundamentals help!
My take on this issue... Blame me for giving theories, A battery and any other electrical load is what it is LOAD, on the alternator. Alternator produces alternating current(AC) and is rectified for Direct current (DC), which contains a part AC which is called ripple, which gets into other electricals and loads. Here in your case alternator whine. an undesired voltage variation to very high voltages (sometimes as much as 25Volts)
Usually in elctronic circuits, they use a filter to ironout these ripple and provide a clean DC. And a great deal of engineering goes into designing these filters depending on the load spectrum and frequency spectrum. Usually a right value of capacitor solves the problem most of the time, but as loads get complex, filter gets complex too. I am not sure if these filters exist in automobiles as battery itself is a huge capacitor and acts as a filter. This may not be new to the guys with ICE experts as I am talking about crossovers.
If you wanna get rid of this whine, curb the ripple. But How?
Frequency domain:
If it is whine, it usually is a high frequency noise (including super hormonics of alternating frequency). Give an ear to the whine, its frequency may be varying according to the rev of the engine. and at a point of rpm, it may vanish. If you find the whine is more at higher revs, choose a lower value of capcitor, and if it is higher at lower revs, choose a higher value of capacitor at the load. I mean at your amp or the HU. (I am assuming you have isolated the thing which is picking up this whine). This should take care of the whine irrespective of battery condition. This may solve Rudra sir's problem.
Load factor:
Above is fine, but why battery changes the charecteristics of the whine? Well different charge conditions pose different loads on the alternator additional to the other electrical loads. Do this experiment. While on the music and the whine is audible, go on adding the electrical loads, loke head lights, AC, rear defogger, etc..Most likely you may notice increase in whine. (keep the engine idling or at constant rpm). While capacitors are good filters they would usually do not live up to expectation at higher load, So use a inductor in series. From alternator to the battery. Inductor block the ripple more effectively at higher loads. In fact, higher the load better the suppression.
PS: I have not suggested any values of capacitors or inductors because the choice of them depends on many factors including the alternator design. It is easy and safe to experiment with the capacitors as mentioned in Frequency domain experiments, but use caution if you decide to experiment with the alternator. This involves identifying the correct DC line from rectifier and cutting the factory wiring.
Enjoy good music
