If the Emperor and the Spacing Guild wanted House Atreides to die why didn't they just kill them all while in transit to Arrakis?

Political intrigue. The entire story was driven by the sub-plot of the Emperor learning via prophecy that House Atreides would bring his downfall.  His power, however, was dependent on the collective support of the Great Houses and that support would have fallen apart if he openly conspired with one house against another.

Killing the family in in transit would have left too many questions.  Murdering just the family would have left too many survivors to extract revenge (and possibly discover the Emperor's complicity).  Destroying the entire family convoy would have required more force than the Harkonens could muster on their own, again pointing to a larger conspiracy.

The whole transfer of Dune was a set up for House Atreides to fail, either for them to be consumed by the hostile planet or in an attack by the Harkonens.  In the case of the latter (which was secretly supported by his own elite troops) the Emperor could appear as the mediator between warring houses rather than as the actual ringleader.  Whatever questions the other houses might have had could then easily be mitigated by large payoffs funded by his complete control of spice production.

Fun fact:  Because of the desert setting and numerous references to Middle Eastern culture, many readers have assumed that "Dune" is a metaphor for the industrial world's handling of oil-producing nations in global politics.  Author Frank Herbert, however, always denied the direct link and instead said his work represented environmentalism in general.... and how political forces often exploited environmental "causes" and manipulation of resources for their own power and enrichment.

Because then Herbert would not have had a story to tell.