That's a pity.
3.5 runs off the 2.0 CLR so it should be just a matter of installing it with the extra libs going into the GAC - sites in IIS shouldn't be affected. You don't even need the option to be configurable from Helm.
See
Scott Hanselman's Computer Zen - How to set an IIS Application or AppPool to use ASP.NET 3.5 rather than 2.0
If there's no way to do it, is it possible to manually move from an old Windows account to the new version without losing the months already paid for?
Are existing customers going to be penalised for a poor setup on the Windows boxen...?