Sounds like a normal scene to come home to after a puppy is left for the first few times.
Consider washable pee pads- they are much thicker and sturdier and tend not to be dragged around and/or chewed up.
Do you have a crate? Lock puppy in the crate or in a bathroom or other small room when you are cleaning the pen- for two reasons, 1. less place for puppy to make mess while you are cleaning and 2. its better if they don't see you cleaning up their messes.
Otherwise, it sounds like your doing everything right. Your puppy will get used to you being gone during the day- right now it just seems like the longest time in the world to her and she is finding ways to occupy herself- she will calm down and everything will be fine
