Are you wanting users to authenticate against Windows Azure AD using only their username (e.g. "mcollier") and not their full account name (e.g. "mcollier@mytenant.onmicrosoft.com)? If so, I do not believe that is currently possible.
If I'm understanding correctly, the app is using ACS as a federation provider to Windows Azure AD. And only Windows Azure AD, correct? If only using one identity provider, what benefit is ACS providing in this scenario?
Is the goal to have the same users in Windows Azure AD as on-premises Windows Server AD? If so, leveraging the new DirSync w/ password hash sync enabled should do the trick.