how dare they contradict how you take it.
Not sure they really thought it through. They may have had one idea, but it ended up playing very differently. Unless Saru is some kind of telepath, he wouldn't know Burnham isn't on that shuttle. On the other hand, he knows what is going on aboard Discovery, he knows how "above top secret" (which is dumb) it all is. It is very easy for the audience to come to the conclusion that something is going to happen to the shuttle passengers. As we see here that lots of people have.