I am considering writing a story where a choice between 2 variables at the beginning leads to 2 completely different branches and I was wondering if this would be possible. IE can play as Bob and has to rescue Sue or play as Sue and get captured.
Sure, why not? As you say, you’ll be writing two stories in one, and have twice the work (although plotting, characters will be somewhat the same), but go for it. It could be a very compelling story.