Hi bradburts and welcome to the forums.
Are you trying to spin down your main OS drive? I've never tried doing that due to the constant log-writing that takes place. I've little experience with trying to suppress these logs so cannot offer any great insight I'm afraid. My OS drive spins 24/7 it's only the "data drives" that are spundown.
Or are you referring to drives in your machine other than the main OS drive? If so, I don't believe webmin or samba cause that (other than other devices on my network keeping the drives awake when connected via samba)
I'd be tempted to follow your suggestion and implement the OS onto something other than a data drive. Or maybe install FlexRAID? With FlexRAID you can RAID just the data you need to protect rather than the whole drive and thus not RAID the logs.
Sorry I can't be more helpful in solving your issue