You question doesn't give a very clear description of your situation, but to me it sounds like you have 1 computer that is running Windows 2003 server, and that at different times there might be a single person sitting at the desk logged in to it to do work. There are several people sharing the computer this way, and there is never any remote connections to the computer.
In addition to the actual Widows Server 2003 server license, Microsoft requires that you have either per-device or per-user client access licenses (CALs) for each device or user that accesses/uses the Windows Server 2003 software. Provided that you have a legitimate OEM/retail/volume licensing agreement, there may have been a certain number of CALs included with your software purchase. For example, a retail copy of W2K3 Standard includes 5 CALs.
Additionally, according to Microsoft, additional CALs can be purchased in 5-pack or 20-pack bundles at a price of about $40USD per CAL, which is not really that expensive.
I think the issue that you're suggesting with the 2-user limit is that there are 2 remote desktop connections allowed for administrative purposes. Additional CALs are required to use the software in a Terminal Server role.
All that being said, you have a couple of options. If you are developing Microsoft-centric software, the best thing to do is to spend the money for legitimate licenses. In addition to retail pricing, Microsoft has various other licensing programs that may be applicable to your situation. You'll need to check with Microsoft on that.
If you are doing non-Microsoft-centric software development, such as web development or Java apps, you could move development to an open source platform that meets your needs. Some choices are Linux, FreeBSD, or OpenSolaris. All are readily (and mostly freely) available, support a variety of development technologies, and don't have the licensing restrictions of Windows Server 2003.