You've already done what this SuperUser questioner is intending to do, and are hitting the problem that xe is worrying about.
The answer is the same.
You've got a combined boot+system volume. This is a poor idea, and something that even the x86 PC world has finally moved away from in the years since Windows XP was released. Windows 7 when installed on an empty system will create separate boot and system volumes.
You currently have your system volume, combined into the Windows XP boot volume, on your first hard disc. As you've discovered, if you remove the system volume (or format it, or make the partition inaccessible in some way), you will indeed render your system unbootable. It is not just a Windows XP boot volume that can be re-formatted or thrown away. It is your system volume as well; and is, as the name says, an essential part of the system.
As you've also discovered, your Windows 7 boot volume isn't directly bootable. It is your system volume that must be bootstrapped by your PC/AT firmware. (This has in fact always been the case for Windows NT. It's simply that before Windows 7 only on non-x86 versions of Windows NT was separate boot and system volumes the norm for installing the operating system. It's now the norm for everyone.)
What you need is a separate system volume, moved on to your second hard disc. What you should not do is have another combined boot+system volume on your second hard disc, because you'll just store up for yourself the very same problem that you are having now, all over again further down the road. Keep the system volume separate from your boot volume(s). It only contains a few things, and you shouldn't need to touch it in normal operation, even for a complete reinstall of Windows 7.
Microsoft provides a lengthy procedure for doing exactly what you want to do. You simply need to use your favourite partition management utility to move things around on your second hard disc, and re-size partitions, to make enough room for a 200MiB NTFS partition at the start of that disc. Then follow Microsoft's procedure.