I work at a Board of Education, within our system we have 12 schools. Each school averages 200-300 computers. Over the years the computers have been set up using various workgroups. We are interested in converting all of these computers to a single AD domain. Is there a way in which I can automate this process from the server at each school? We are using Windows Server 2003.
Firstly, there's way more to setting up a domain than just adding the computers to it. You need to consider how you are going to setup your Forrest/Domain structure, security, DNS, account/ computer creation, amongst numerous other things to just get started designing this. Also, the profiles you are referring to will still remain on the workstations. After being joined to the domain, the new accounts will just create new profiles. You can still use tools to copy over old profiles to the new profile.
You shouldn't try tackling this if you don't know what you are doing. Hire a contractor or full time sysadmin to design and build this for you.
It can absolutely be done, but you should want it done right, especially in a school setting.
To answer your specific question, there are ways to "automate" a join to a domain. Such as using sysprep and an answer file, but you would still have to image the computer. You could also use a script to do this.
Also, you should try to avoid creating this domain with windows server 2003. It's support ends 7/14/15 and although that's still two years away, it would be nice to avoid having to upgrade later.
I would suggest you image the computers either way it goes. Gives you a fresh start with the workstations plus nothing "ghostly" will be out there. Also something like Altiris may give you some benefits as you can image computers remotely and do many other tasks. I know of several schools using Altiris to help them out.