Question: Can Exchange 2007 auto-reply to an incoming message? I don't want to set it up in Outlook, I want the reply to be done on the server.

Answer: 
Out of Office auto-replies are setup within Exchange, and reply to any incoming messages- not sure if that's what you are looking to do?
If you still have a public folder database mounted and online, there's a neat trick for utilizing a hidden public folder. It should be noted that while Outlook is used as part of the configuration process, Outlook is not what drives this, it's server side config like you are looking for.

1. Create the public folder and and remove visibility for default users (but make it visible for you so you can perform the below steps)
2. Mail enable the public folder, and give it the email address that you want senders to use
3. In Outlook, navigate to the public folder, right click and choose Properties.
4. On the General Tab, click folder Assistant

Here you can build the rules to auto-respond to the sender as well as forward on to a distro and then remove the item from the public folder. If you set up a response, it will launch an email template that is saved at the top of the information store for that public folder.