Not sure what this has got to do with using a Harmony remote or not...
Edit: wait, do you mean "Hd doesn't spin down or turn off when the BB goes to sleep" (which is a slight but important difference due to word order

)
In which case, there are limited choices:
1) leave the BB on (or sleep mode which doesn't save you any power anyhow) along with the external drive (why not? I have 7 drives on 7x24 in my WHS system)
or
2) power off the BB and turn it back on via the BB's own power button or via the Boxee remote.
That's it.
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