If I understand your requirements, you won't be able to use WUBI in the way
you're wanting to. WUBI isn't quite the same as a virtualized installation of
the OS and so you can't run it from within Windows. Basically, WUBI acts the
same as if you'd set up Ubuntu in a dual boot environment: at system startup,
your user would have to choose to either boot into Windows or Ubuntu. Once they
are in a particular environment, they will need to restart their computer and
choose to boot into the *other* environment in order to switch.

I think someone on the group suggested virtualization and I'm going to recommend
that too. Usually when my clients have needs like yours, virtualization is the
route we take. Using something like VMWare, you could put a fully configured
virtual machine icon on their desktop that they click on from within Windows and
can run the Linux program they need from a full install of Ubuntu.

Keep in mind though that virtualization requires that your machines have enough
resources to support *both* operating systems running at the same time so it may
require some memory upgrades.

Alternately, you might try cygwin. It's an emulation environment that gives you
a full working Bash shell from which you can run almost all command line
applications. It's *much* less memory intensive and would probably be your best
bet in this case. Of course, since I don't know your specific requirement, I
can't really recommend anything specific but those are your options.

If you have questions, please feel free to get in touch or hit the list again.
It's a great resource with some fantastically knowledgeable people.