Lady Jessica was supposed to be "given" to Piter de Vries once she was captured. It is only once she is in front of the Baron and Piter that the latter renounces to have her and instead chooses to reign over Arrakis. It is then that it is decided that Jessica and Paul would be sent into the desert.
So how could Dr. Yueh know in advance of this, since he left a package and a note in the ornithopter beforehand, and told the Duke he would save them? Also, a deaf guard is used because of the Voice, so how could he possibly know they would survive?