(With the caveat that David is doing the vast majority of the writing, and that these are just my thoughts on this.)
The thing about choices like that is 1) either they don't actually matter very much (i.e. you end up with "you made a big choice, and are now funneled back into the main narrative regardless" kind of thing), or 2) you end up with an exponentially exploding number of combinations that's entirely unmanageable. I'm not really a fan of the former (presenting something as a major decision, and then mostly ignoring it), and the latter is just non-viable.
To your example, stealing a macguffin and deciding who to give it to feels like it'd be a clean fit for a single mission. But put that into the beginning of a story, and... I'm just not sure how you get away from either essentially ignoring the choice, or writing a bazillion variants of everything further down the line from when that choice is made. And I don't think you can really have a compelling narrative that also allows for a lot of major choices like that, what you'd likely end up with would be more akin to madlibs.
I mean, there'll be choices! Options for dealing with various situations in different ways, ways of expressing how the player character feels about things at various points, and so on. Just, within what actually feels reasonable while actually still having a story arc.