So after four months my prediction has come true - the fact that my new employer has a single level domain name has really turned and bitten us. We need to deploy Lync 2010, but can't deploy it in a domain with a root SLD.
Domain renaming is not an option as we have Exchange 2010 deployed.
The only solution I can see is to set up an entirely separate forest in which to deploy Lync, set up a forest trust, and over time migrate everything from our existing, legacy forest to the shiny new one (which is what I wanted to do anyway, but I'm keeping quiet about that).
Has anyone got any advice on doing something like this?