To a ScriptFrenzy forum member whose minor character was hijacking her drama and making it a comedy:
I gave your quandary some thought today, while avoiding my other projects in the 106-degree Arizona heat.
I have set an odd pace for this thing. I write for a couple of days in a burst, and then I step back and look at the big picture for a day. It's somewhat unusual for me, but it seems to work. There's always the guilty tension of stopping for a day, and the fear that there won't be anything when I get back to it. Then I read over what I have (being careful not to edit), read the burgeoning synopsis, get images and ideas, and the next day write a thousand words.
The day off seems fraught with danger, because my first impulse is, like a shark, to keep swimming at all costs....
Character take-overs...my thought is that they are good, they show where the energy is leading, and are worth pursuing but only if they serve your big picture, what you are trying to say. If not, then either you have to take the situation back in hand or you have to change your big picture. It is a balance, unfettered creativity vs structure, seat-of-your-pants vs the outline, and I would be very surprised if there aren't half a dozen forums devoted to this problem already. (I haven't looked for them.)
Anyway, my big picture work today was to finish reading Syd Field's Screenwriter's Workbook to get some idea of how to best arrange my Act II. And he addresses your problem in part in the chapter on Act III: "If you experience any resistance, doubts, or judgements, just 'bend with it,' acknowledge it, and continue writing....If your ending comes out different from what you want it to be, write it one way, put it away...and then write it again; this time it will be the way you want it....[If you're writing a drama and] it comes out funny, write it, stick it in a drawer somewhere and forget about it, then go back and write it the way you want to."
My other thought about tone is it is a lot like theme. Stephen King is a seat-of-the-pants writer, and he says he doesn't even know the theme of his piece until he has--you guessed it--finished the first draft.
Hope this is a help. I may have melted too far to give sound advice :)