Is he trying to hurt it? looks like he at some point pressed the pencil into it's mouth.

That is the hamsters doing.

I don't believe in the myth of hamster-organs. I believe that hamsters are just little balloons of furry cuteness, and that is why the pencil is just poking right through its little face.

In case you didn't know, hamsters can use their cheeks as pockets for storing stuff.
They can hold about two or three dozen sunflower-seeds...
I think, if the pencil was chopped into bite-size chunks, they would all fit in that little critter's mouth...

why is he trying to store the pencil anyways?

I know they store food because they're greedy. Cute, but greedy. Maybe it thought that if it stored the pencil it could store anything.. Like some kind of test.