I am not sure of exactly what you face in the way of difficulty, but I
will say that creativity and being stubborn can do wonders.
Along with careful planning of course.
Case in point-
Water Cooled mATX LAN PC
Crammed inside that case is a radiator, pump, dual 120mm thin radiator, two 80mm intake fans, a watercooled cpu, northbridge and water-assisted full size ATX power supply, along with a cd burner and hard drive.
I may have a few advantages in that I have done a few H2O systems and heavily modded computers as well, but...
You may be able to fit everything if you REALLY want to-
You may have to sacrifice a few degrees for the mobo and/or cpu to do it, of course...
An internal pic of the system as planned (with mobo and cards, etc) would help.
BUT- to answer the original question:
Yes, mounting your pump on top of the case will be fine- location really matters little in a closed loop. What does matter is how tight the bends are and how restrictive the system and fittings are.
An alternative to this would be mounting your radiator externally- this would probably free up more room in the case, and get you an improvement in temps as both intake and exhaust to the rad never enter the case.