There is no way that Hitler would have gotten away with assissinating the Pope, his own troops and SS would have turned on him. Many of his soldiers and SS were (no matter how Satanic their actions) were devout Catholics and revered the Pope and would never have countenanced murder of the Holy Father. It would also have galvinized the rest of the world against him as well all the more. Mussolini would have turned on Hitler in a heartbeat.
Some members of the Wehrmacht were. SS, not so much, although there is an interesting memoir written by a Catholic seminarian (later a priest) who ended up in the SS. (His SS superiors all thought the SS would "cure" him of his Catholicism. Didn't work.)
As to what Mussolini would have done ... interesting question. And the Italian people themselves might have risen up in guerilla war against their German occupiers.