There is no current known way of doing this. There are things we can do to represent civil war, but we cannot allow the player to choose sides. Largely because we cannot allow the player to choose their heir.
Foot
I recall in Medieval TW always if coup d'etat occured you've been asked: do you back the rebels???, so I thought it is possible in RTW/M2TW as well but apparently it is not. Anyways it'd be quite intriguing to have such option.
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