Most of us have moments like this when writing. We're forced to take out characters we love or put in elements that we don't want. There's no changing the path that our plots are predetermined to follow. From the moment we start that first sentence, we've set in a motion a chain of events and circumstances - many of them well beyond our control.
I'd tell you what the realization I came to is, but as River Song of Doctor Who says: "Spoilers, sweetie."
What plot twists have you point in your writing that you weren't entirely happy about?