When it comes to shipping, my personal opinion is just as long as you're civil about it, ship away. We all have characters that we feel are good pairings with each other, even if they aren't paired in the story, and it's OK to express those opinions. Just don't shove those opinions in others faces or denounce theirs for holding a different one, because no one wants their preferences attacked and there shouldn't be a "war" to decide which character should pair up with who when it's left open to interpretation.
In short, live and let live, ship who you want and just respect others for their personal choices.
