Long winded rant ahead.
*clears throat* Hello all. My name is Gay_Vampire and I'm here today to talk about a widespread and frustrating problem among fanfiction writers today. Namely, dealing with Characters You Don't Like. Now there is nothing wrong with disliking certain characters, as it's your own opinion and the rabid fanbrats probably won't find out about it and promptly rip you limb from limb for the unforgivable crime of disliking a certain character.
However. One day you may be struck by a bolt of inspiration. Excited beyond belief, you promptly ignore everything else in life and dash to the computer, intent on showing the world your genius. But alas! Midway through the writing of your glorious fanfiction you have encountered something. A scene that no matter which way you twist it, absolutely must have a Character You Don't Like starring in it. Oh no! What will you do? How will you deal with this threat without pissing off the legions of rabid fans? Worry no longer over these agonizing questions, for I have the answers. Or at the very least, vaguely helpful suggestions.
How to get rid of Characters You Don't Like.
1. Ignoring them. Simply erasing all traces of the Character You Don't Like is an appealing concept, but difficult to properly pull off. In the case of minor characters you can use this but with major characters it is unadviseable, as many of your readers will become confused/enraged by the absence of said character and promptly send you angry emails declaring "Why isn't {character A} there?! {He/She} would be sooo much better at foiling {designated antagonist}'s evil plans than that idiot {character b}!!". If all else fails blame Namine.
2. Killing off the Characters You Don't Like.
ex. Sora gazed forlornly at Aladdins grave. 'If only I had been here sooner...' He shook his head violently, attempting to remove the disturbing thoughts before they took root. "They will pay for this." He growled, gripping the Keyblade firmly as he stepped towards the palace.
As you can see in the example above killing a character off can be beneficial to both you and the plot, as now your intrepid hero has even more reason to hunt down the nefarious villian. But if handled poorly it can seem like nothing more than a grab for cheap angst, so be careful when using it. You also need to be careful about the other characters reactions to the death. For example, if Kairi suddenly died in an excrutiatingly painful manner, it is important to remember that no matter how much you want him to, Sora would not cheerfully screw Riku on top of her grave whilst singing "DING DONG THE BITCH IS DEAD!"
3. Providing an excuse for the Character You Don't Like to be gone.
ex. "Well gawrsh Sora, I'd love to help but I've gotta train the new recruits 'fore I can get anything done." Goofy scratched his nose, grinning sheepishly. "Maybe next time though?"
Quick and painless, this is by far the best way to get rid of Characters You Don't Like.
And that's pretty much it. Sorry for the tl;dr.