First, how do they managed to enter? They lacked artillery, and the lack of real command prevented to make such an action easily (without talking about how it was more profitable to plunder easily the city rather than go trough a military action).
Assuming they did, Charles V is going to be in a really bad position. His troops outright killing the pope is going to send a message such as "The emperor doesn't control his own troops and he's ready to launch these for pure chaos purpose".
Either it means he would have to retain himself in his foreign policy, in order to look as compromising (and certainly have to punish, as in decimate, his own troops).
It would be a clear boost for France foreign policy along the lines "Hey, even Turks are more civilized" and maybe out of fear from neighbouring states. Francis would have it easy, just pointing this.
He could try to create a pope of his own, but it would look barely legitim : an antipope would likely appear (supported by France, maybe by England as well), and it would look more legit. I think Charles would refrain to do that (but it may cost him a quick recovering of the imperial crown).
Religiously, it would be as well a boost for german Protestants.
The main beneficiers would be both Protestants and France, and Charles would have a lot of issues not only on its italian policies (while it may likely force a more peaceful status quo, out of fear. But frankly, that an army disobeyed his orders to kill everyone up to the pope isn't going to tell much on the strength of his authority) but as well in Germany itself.