Maybe you could create a SOPC Builder component with a single slave interface, which only has an IRQ pin on it? If you don't give it any HDL source files, it will just export the IRQ pin to the system module. Then you just have to create as many of these components as you need interrupts, and it's like having external IRQ pins.
You'll need to rebuild the SOPC project and chip, but I don't think uClinux will need rebuilding (since there is no new address space taken and you don't have to initialize PIOs). Then you just have to hook in your interrupt handlers, and you should be good.