Firstly, I agree with Jeff. Connecting real time systems to the internet is not a good idea, especially if they're critical.
Secondly, on Deep Freeze - according to the wikipedia article:
Deep Freeze is a kernel-level driver that protects hard drive integrity by redirecting information being written to the hard drive or partition, leaving the original data intact.
In terms of the impact on your system this means that writes look like this:
---------------------- ---------------------
| Userland program |<-----Read--------| Kernel | |-------------------|
| e.g. explorer.exe | | |-|-------------|<---Read----| File system |
| or something else |<-----Write--| | | Deep Freeze | | | i.e. directly to |
---------------------- or read of |------| Driver | | | block device |
modified contents | |-------------- | |-------------------|
| /|\ |
-----------|---------
| Write/read changed content
\|/
----------------
| Some form of |
| temporary |
| storage |
----------------
So any modifications you make using standard IO routines will be redirected to a temporary storage. Reads, as I understand it, will also follow this if the content is modified, otherwise loading directly from the file system itself. When the system is reloaded, that section is forgotten.
How effective this is depends on the level of penetration. Inside the kernel, if you use the hooked routines to write files, your writes will be redirected too. However, kernels can write directly to the disk and will contain code to do that, so unless you patch all of that to remove it, it is feasible to write to disk. The intercept is likely to be higher up than that, mostly because that'll catch 99% of all calls and because it is reliable.
Where can I obtain reasonably relevant boot sector viruses for testing?
Now, the crux of the issue. Deep freeze's write protection only works once loaded. So you are correct in your assumption that if you load code before deep freeze standard routines will work for you just fine. You could even load a filter at a greater priority, intercept certain writes and persist them before deep freeze even sees them.
As to finding code that would get you started, vbootkit 2.0 was a proof of concept (aside from inserting itself it didn't do much) "bootkit" designed to compromise windows vista x64 pre boot. It has disappeared from the internet on looking for it this evening, but if you can find a copy, that will give you a starting point. It is, however, complicated. I'm writing a filter driver right now (blame AviD) and getting it right is hard. I don't know of any code that deliberately targets deep freeze specifically, though.