For me that sometimes that's just what happens. The last time I sat down to write a D/s story it started from a simple seed of a pair of characters and an interesting setting. I thought I knew where it was going, but when I actually sat down to write and let the characters flow, they ended up in quite a different place. Instead of a simple naughty tale with supernatural elements and a crescendo of bondage and submission, it became something more Austen-esque, a melodrama starting from a supernatural setting but in the end being more about these two strong characters and the tension and thwarted love between them. I didn't even get to the bondage part
So yeah, sometimes the story has its own ideas, and it's better to go where it feels right, than to try to force it into the shape you originally imagined. Take for example
Scare Me by Zephyr published recently. Erotically charged throughout, but the ending really could not be anything other than what it was, not erotic, not happy, just acknowledging the most likely outcome of events like that. If you altered that to be some sort of happy ending it wouldn't ring true, you wouldn't believe the character's motivations.