This method involves utilizing the File System Table (fstab) for the BSD subsytem.
Yes, thank you orwell! This is the best solution so far... As the original poster learned.
An improvement to this suggestion would be to use the volume UUID instead of the label. It's a more secure method much less prone to breaking (like if you end up with more than one HD with a "System Reserved" partition on using the UUID is the only thing that works). But that's a bit more tricky since the Disk Utility does not display the UUID for NTFS formatted partitions (thanks Apple!). However, this doesn't mean there isn't one. You can learn that with the command:
diskutil info /dev/diskXsY ##substitute X & Y for the disk and partition numbers which you can learn with the command: diskutil list
This command will not succeed if you have a 3rd party driver installed for NTFS (Tuxera or 3g are two that come to mind). You must disable any non-apple file system drivers for the partitions in question and reboot.
You must also either have the partition mounted or dismounted when you run the command- I don't recall which but I remember it being the opposite of what the tutorial actually said.
If you still can't determine the volume UUID, you can use an Ubuntu installation disc to boot into Ubuntu and there are a number of ways to reveal the UUID- gparted is one.
Then add the following lines to fstab as described by orwell:
UUID=(you know what to paste here- no brackets or anything) none ro,noauto 0 0
reboot and viola! no unwanted partitions...
As you've most likely learned, the orange icons issue is almost certainly just a cosmetic thing which can be "solved" in a number of ways- however, it will not affect the functioning or performance of your system or disks.
Anyway, I hope this helps someone at some point. It took me a long time to figure out how to reveal the UUID despite the simplicity... And although it is merely a cosmetic thing, and I've developed some work arounds like scripts that unmount the volumes, etc. But this is by far the cleanest and most effective solution. And very simple once you know how...