You can set the key in the users registry to prevent the warnings. You should only do this if you know what you are doing!
The attached file has three registry keys I change for my users with a Windows XP computer.
DisableSandboxMode.reg
SetAccessFileFormatTo2003.reg
SetAccessSecurityToLow.reg
The user must have admin rights to the computer to edit their registry. If you launch the reg keys with the silent option the user will not have the option to abort the changes so you know it is done. I use a custom .exe program to run the regedit during the installation of my applications. Here is how you would call the regedit from the Run command.
REGEDIT /S \\Server\Partition\Directory\DisableSandboxMode.reg
You could [should] export your own keys to ensure that the system settings are correct for your companies computers since some companies do not use the standard default installation locations for Office 2003.
You are at your own risk for using the attached files to edit the registry of a Windows XP computer!