I have never had any problems when doing a similiar process under FreeBSD using cam control but I don't know about IDE devices. When you power down the drive does it truly power down like a SCSI device?
As long as any buffer in the HD is commited to the filesystem before removal you should be ok but I am not too trusting of IDE. It really wasn't meant for that.
There are hot-swappable IDE cards made by Promise though, but I do not know of their level of Unix support.