Just some thoughts, take and leave what you will!
Yuyuko - Remember she also has the ability to manipulate the spirits of the dead, not just kill people. I don't see this having a very happy ending, but you could always do something like she pushes herself to get the 'instant kill' power in order to save someone/thing/place.
Flandre - She doesn't have to break people, she can break things too. And even if she uses her power on people, it doesn't necessarily have to kill them. Maybe in a fit of rage/panic/by accident she crushes someone's arm or leg or something. That would still be a pretty powerful experience to someone, especially if you are writing them to be as young as Flandre (visibly) is.
Utsuho - Blowing things up doesn't have to be violent. In her case, it probably will be, but if you are creative you should be able to do something good with it. I find it hard to imagine the kind of things Utsuho could do with her powers that wont get people killed though...fission and fusion have a pretty narrow range of applications, and they all seem to be on the 'way too strong' end of the spectrum. This is probably the one I would find most difficult to adapt into your story unless you were willing to play around with her powers a bit, and make her slowly work her way up to Nuclear-level phenomena.
Hina- She's a goddess of Misfortune, but that's because she takes people's misfortune away! She's almost perfect for a more lighter toned story, because her power is based on making the people around her happy. If you don't mind playing with canon a little bit, you could write quite the tragic heroine story about her taking people's misfortunes onto herself (canonically, the misfortune doesn't affect her either, but that's the great part about fiction :P)
Remilia - This one will likely end in a much sadder tone. Assuming you don't push the vampire angle and you just focus on her ability to manipulate fate, you could write a very compelling Icarus-styled story for her. She figures out her power and decides to put it to good use, but gets in over her head and things just don't turn out the way they were supposed to. Alternatively, you could write a more Haruhi-esque story, where she has no idea about her powers and the focus is on the people around her dealing with her unconscious manipulations of fate. This has more potential for a more light hearted story, but with some creative writing both could go either way.
Orin - If you want to stay away from the grim, darker parts then avoid her passion for dead bodies completely. Similarly to Yuyuko, she can control and communicate with the deceased - your imagination can take you pretty far writing a story like this. And remember they don't have to be the recently deceased, nor do they have to be angry, vengeful ghosts. Maybe she makes it her life mission to help the lingering dead pass on peacefully? Only you can tell us!
I tried to avoid going into too much detail, because its more fun if you come up with the core plot points on your own, so I hope these brief blurbs are enough to give you some ideas!