They DO make cards with the heatsink assembly on the other side.
But really it makes less sense than revers ATX which has already been mentioned, having the cooler on the other side for a desktop means sucking hot air from the CPU/Memory side, when really it's cooler on the otherside. For a tower, buy a reverse ATX case, they're not expensive nor hard to figure out and you have the benifits your want.
Current design will persist as long as HTPCs and other use generic desktops that benifit from that flow, the need for inverted sooling just isn't there anymore, especially if your HSF assembly works like the HIS and draws the air out of your rig, you don't want that sucking waste CPU/Mem air either.
Best solution would be a 2 stage cooler that drew cold air in around the units and then back out again, but that'd be an even bigger cooler to achieve the same level of airflow.
And HIS style cooler with an AGP intake porthole on your case wold be best IMO, and best the way it's currently designed.