It's hard to understand what is going on with them and not it will become interesting. They extended Guardiola's contract and it would be ridiculous if they sack him weeks later, so I suppose they are going on with him no matter what's going to happen.
Sacking Guardiola will be a poor decision because this is only the first time his team has struggled this much so if the team doesn't trust him in a time like this, it means they don't deserve him. As you said, it's difficult to explain what is really wrong with them, but we have to remember that Rodri was not the only player he missed. He was without KDB, Doku, Grelish, Ake, Dias, and Stones at a certain point in this season.
I believe with a few players in strategic positions Pep can get his team back to winning ways. Players like Walker and Gundugan have failed to live up to expectation so people shouldn't regard them as top players. KDB has been too injury prone to be at top level. Worst of all, Pep's system relies on a DM and without a reliable DM they'll struggle.