The interrupt controller device tree fragment should get added automatically by the device-tree fragments PYNQ adds in its Yocto recipes. You can edit this if necessary. I would say that this only needs to be done if you’re planning on accessing interrupts from PYNQ.
Note that there is no support for reprogramming designs containing the interrupt controller in the Linux kernel so if you’re planning on doing full bitstream programming you’ll need to hook anything used by Linux directly up to the PS and then use the interrupt controller attached the interrupt line under the control of a UIO device. Note in this case you don’t put the interrupt controller driver in the fabric.
The hangs you are seeing look suspiciously like those when JTAG is being used to access the board. Can you try the steps in this thread and see if it helps.
Peter