Personally, I don't believe that we are witnessing any bias from the journals as written from the perspective of "the good guys." I think what we hear in terms of flashbacks and live action (whenever a character isn't narrative events as they specifically read them from a journal) is going deeper than what is written in the journal. In other words, the journal is a device that allows other characters to be witness to things they weren't there to experience first hand, but the moment the story cuts to those moments, we are hearing them as though WE are there first hand; a silent witness of sorts.

So although the writers of journals could put their bias into the journals, I do believe that we the audience are seeing things as they actually happened. So our opinions as to whether Scratch is evil, misunderstood, crazy, sane but cruel, or whatever are totally up to us. I doubt we are being affected by the feelings of the journal writers.