You've got to get ahead of it. You have to find out right now, to the best of your ability, if Lion is going to break anything that your users need. You need to consider the security aspects of Lion versus whatever version of OS X you're currently running, and whether you're comfortable with handing over security updates to Apple's Mac App Store timetable. And, frankly, you need to decide if the extra functionality afforded by Lion is enough to overcome the extra headaches that IT will likely endure in the short term, and potentially in the long term.
And then you need to clearly assert your position. If you're good with your users upgrading, let them know. If they are not to update in any circumstances, let them know--and your reasons why. If you need them to hold off until you can test Lion and make sure it won't break anything for your business, let them know that--and keep them apprised of the decision-making process.
Under any and all circumstances, you need to communicate expectations and reasons with your users. But let's be honest: This is especially true if you want them to hold off, either temporarily or permanently, from making the move to Lion. And you need to do so well in advance of them getting the first chance to click on the Mac App Store and self-update.
The need to have a well-communicated plan and policy is clearly the most important decision. But there are a number of other factors to consider as well.
Even if you have made the decision that you're going to go for it, and full on day one let users update to Lion, you need to be aware that because it's only distributed through the Mac App Store--which only runs on the latest version of Mac OS X 10.6 Snow Leopard--any machines not running Apple's latest release are not invited to the party.
Sure, Macs are more likely to be running the latest OS as opposed to the Windows world where "wait until SP1" is practically the Golden Rule of IT. But if you have users on Leopard or earlier, they need to know that they can't directly go to Lion. Consider the pros and cons of making the upgrade from the aging OS to the new one. If it makes business sense, make a plan first to get them to Snow Leopard, and then to Lion. Or, if it's coming up on hardware refresh time on the machines running the older operating systems, consider waiting until new machines are shipping from Apple with Lion onboard, and then just migrate user apps and data when setting up the new computer.