Take a look at this previous answer for some discussion on this topic: Exposed onsite vs IFD deployments for MS Dynamics CRM
I would say from my standpoint the biggest issue with using Windows Auth over the internet for CRM is the issue of Outlook integration. The second point I would make is that Windows Auth can present issues to people accessing CRM from a non-domain computer when outside the domain - i.e., their home computer. Not always but I have seen issues pop-up (not very often) that are avoided in a forms based configuration.
As a reminder in 2011 the IFD feature has been changed signficantly so that you must use Active Directory Federation Service which is claims-based. I recommend reading over http://blogs.msdn.com/b/crm/archive/2011/01/13/configuring-ifd-with-microsoft-dynamics-crm-2011.aspx and watching the video at http://www.youtube.com/watch?v=ZD5qaa-G99E.
You can certainly go with Windows Auth but if you are willing to put in the extra work go with the Internet Facing setups for a more robust and better supported install.