I've got two machines in this situation, one of which is SL/3.2 and one Leopard/3.1. For the one project that I share between the two, it seems to work. But as Mark points out, there's no guarantee that it will work in all cases.
I have not tried this, but it may work to have you use the project file in 3.2 and your partner use a 3.1 project file. Don't check it in, only work with the source files from source control, keep your project files local. I've done this between versions of Visual Studio, which is what prompted the idea, but though it sounds good in my head I've no idea how well it would work in practice.
Another alternative is to keep two versions of Xcode on your machine (search SO or iphonedevsdk.com for the how-to). I've done that through the OS 3.0 betas, but that assumes Xcode 3.1 lives happily on a SL machine. Probably the safest one to try, as the worst would be that 3.1 won't install or run on SL.