I would recommend reading Gene Luen Yang's Boxers & Saints for perspective on how someone else has dealt with this question. It depicts the same historical conflict through the viewpoints of a main character on each side.
I'm normally not a fan of alternating viewpoint stories, but this seems like a good case for one. It's hard to see any other way of doing it that isn't clearly picking sides.
Maybe pick two main characters who are initially childhood friends (across religious boundaries), but end up on opposite sides after the partition. You might not have to actually do alternating viewpoint if you build enough empathy for the non-viewpoint character. You could even do a Romeo-and-Juliet interfaith romance, if that is of interest to you (however, that could anger people for other reasons).