Together with some others at android-hilfe.de I'm working on an overlay filesystem for the Desire.
We've chosen aufs (Another Unionfs) to implement our idea.
Basically, two filesystems are combined to a single one.
The first filesystem contains the initial data. The second one is used to overlap it.
Aufs first searches the second for files, then the first. We plan to use a fully writeable filesystem for the second and a secured filesystem for the first.
If you want to modify a file on the first partition, you can put it on the second filesystem and change it there.
So we can get indirect write access to the secured filesystem by mounting the aufs partition to the right path so that the system sees it as the original, secured filesystem.
In theory, a full r/w acces to the all partions on the phone could be possible.
Visit the project site for files and instructions.