Sometimes enthusiasm for Linux and Open Source can overcome good sense. Linux is ready for prime time withot question from a technical perspective, but that doesn't mean your users are. The message coming across loud and clear from various projects is to avoid a "Big Bang" approach. Roll Open Souce out gradually, moving users to Open Source applications such as Firefox and OpenOffice first, and only later changing the operating system. Changing everything without consideration will end up with a bad result for everyone, and turning people off of open source.
This story is not unique. At least one other major site in New Zealand that converted to Open Source reverted to Windows due primarily to the effects of a "Big Bang" role out. Rolling out a large deployment that makes use of technology in new ways is bound to introduce issues. Sadly these issues can double up with peoples fear and dislike of change to result in a user base that turns hostile to the solution.
To avoid this outcome there must be due consideration of the changes users must deal with. A role out starting with new applications used in parallel at first given to a limited pool of users will build a core set of users with expertise. As more users are moved from applications they are used to they will have others to help them.
Only once the applications have been migrated should there be an attempt to move people off the operating system. There is nothing worse than users who are unable to do their job because the IT people have not considered the users needs.
One of the core approaches within an organisation should be to embrace only technologies based on open standards. Use IMAP and POP3 and SMTP for mail for example. Where possible use web applications that do not need IE specific plug ins rather than fat client Windows applications. Use applications which a cross platform, ideally based on languages that are cross platform.
By supporting a technology policy that encourages choice any change in any one peice of that technology will no longer be a painfull experience. Moving away from vendor lock in may require some planning and care, but the long term benefits associated with choice and independence will offset any temporary discomfort.