I think you would do fine with the Zalman harddisc heatpipe cooler, possibly with some slight modding.
There is no problem with generating heat on both ends of a heatpipe.
When the fluid in the heatpipe warms up (at both ends in this case) it turns to gas and start to raise to the highest point in the heatpipe. In this case this will be the middle of the heatpipe in normal mounting. So the middle of the heatpipe will act as a small heatsink. As soon as the coolant cools down a bit it becomes a fluid and it starts to sink down again.
If you want twice the efficiency you can mount 2 of these harddisk coolers. You would mount one on each side of the harddrive mounted outwards like this:
|-----| HDD |-----|
This will make the enclosure quite wide, but still keep it very low.
Note that the Zalman cooler comes with press-fit only, so the efficiency can be increased a lot if you put some cheap TIM between all contact areas. E.g. HDD side to aluminum side and at all ends of the heatpipes.
I think you should be able to keep your harddrive in the 45*C range with this low cost passive cooling.