It will be faster in most things unless the Quad-core gets saturated by the available bandwidth.
The i5400 and the old Bensley motherboard used in the Mac Pro has what is know as DIB, Dual Independent Busses. One for each processor.
Apparently someone on this very board received his single Quad-core Mac Pro.
It retains the other processor socket but no heatsink.
It should be doable but you still need to find a compatible heatsink.