Você pode configurar o gerenciamento de energia com
hdparm -B $value /dev/sdx
Coloque isso, por exemplo em /etc/init.d/boot.local
Citando a página man:
A low value means aggressive power management and a high value means better performance. Possible settings range from values 1 through 127 (which permit spin-down), and values 128 through 254 (which do not permit spin- down). The highest degree of power management is attained with a setting of 1, and the highest I/O performance with a setting of 254. A value of 255 tells hdparm to disable Advanced Power Management altogether on the drive (not all drives support disabling it, but most do).