1) Is it possible to enable/disable interrupt (i.e. __enable_irq or __disable_irq for ARM) in the userspace code of sel4? 

We want to make sure that the execution of the code in the initial process does not get interrupt.

No. However if you assign your interrupt handler a lower priority than the task that you do not want interrupted, the handler won't be scheduled. This doesn't stop the irq handler from running in the kernel, but the notification won't be delivered until your lower priority thread is scheduled. 

Adding to what Anna said, as I’m not sure we understand Oak’s question correctly:

IRQs remain masked until acknowledged, so by delaying acknowledgment you can prevent the interrupt re-occuring (and the low-level kernel handler being invoked).

Gernot