The pump is no problem. Confusion about it is people think an Eheim can make noise. They don't, but they do vibrate. If this vibration gets transmitted to your case, it starts resonating, and your case gets noisy. So indeed, rubber bands are ideal to decouple it from the case. I put it on a couple of layers of soft plastic foam to insulate it from the case. Pump is inaudible with the case close.
About those aqua-computer hdd cases: I've read from several people that they're really good. Problem is indeed, they're aluminium, and although eloxated, one scratch in the elox is enough to start the slow decay of your coolers. You'd need to use aquacomputers additive to counter that. But such hdd cases exist in copper too:
http://www.heatkiller.de/ and look in the shop for silent star hdbox.