Yeah my takeaway, and I think Duke may have even mentioned it, is that they knew by going to Arrakis they would be vulnerable and exposed versus the safety of their home. But, I believe the suggestion is that they had to go because for centuries the pact is that if the emperor gives you a fiefdom you have to take it or risk all the houses turning on you.
It seems a little far-fetched, given the safety of their home planet, that the doctor's/traitor's wife would be both taken and taken in a manner that nobody but the doctor seemed to know about it. Seems a little far-fetched that the Harkonnens could both get to her and get to the doctor fast enough before he could tell the Duke or somebody with authority in Atreides. However, I think it's generally plausible enough that one can go with the stretch needed to create the plot point.