Dank,
Because the server is not a quad core
If it was, I would say yes.. you'll likely get better performance with it according to the limited information before me. Again, before I'd feel comfortable offering a prospective customer an upgrade solution - I'd really like to be able to see output of iostat and vmstat at bare minimum.
Server option "B" is a single processor, dual core for a total of two CPU cores @ 2.4Ghz. Server option "A" is a dual processor, single core setup for a total of two CPU cores @ 3.0Ghz. The Core processor is better, but not by a mile. I would go as far to say as you'd see fairly similar performance characteristics in the real world given the two options, with the Core beating the Xeon by a tad.
And yeah, ideally here you'd simply go all out and get a server w/ both disk and CPU. Something like a Dell PE2950 or similar (e.g. 4 or 8 CPU cores total, and SCSI disk). Granted, that's expensive.
And the difference between an old 2.4Ghz Xeon and a 3.0Ghz will be decent. The CPU's on the two machines listed are "roughly" similar, so I'd go with what has the better disk subsystem.
-Phil