Buy the server with the L5320s, you can easily buy a pair of L5420s later for dirt cheap, and you'll appreciate the extra RAM. Set up ESXi, don't just run directly on the hardware, there's no way one linux install needs 24GB of RAM. Believe it or not, the biggest source of lag with that setup will be hard drive throughput. ESXi makes it easy to track this, and I frequently see spikes in hard drive queue time, which means lag for minecraft. Having 24GB of RAM you can easily use ramdisk for minecraft.
This server... Is it a supermicro by chance? I own the exact same one. You can fit a 2nd drive in it if you're creative.