I've used both, but with that many computers / users to support I'd lean toward Windows Server to get both Group Policy and Windows Server Update Services. Both of them are going to make your life easier and decrease the amount of support labor related to client computer maintenance. If you haven't read up on what Group Policy can do, have a quick look at: http://serverfault.com/questions/66049/what-group-policies-have-you-applied
A lot of people focus on the "locking down the computer" uses of Group Policy, but for me it's about automating administration tasks and making new PC / user provisioning consistent and as near to automatic as possible.
Will it be worth the added expense to go w/ Windows Server versus Samba? That depends. I think the TCO savings would be worth it, but those certainly aren't "hard numbers".
It will be easier for the organization to find somebody to maintain a Windows Server installation when / if you decide to move on. (That's not to say that maintaining Samba is particularly difficult, or that the average Windows Server admin off the street really knows what they're doing, though, either.)
To be fair, you can use scripting to do anything that Group Policy can do. It may not be as easy, but it's certainly possible.