You wrote: " In keeping with the Prism ideals, one would not directly use the Entity Manager in the View Model but rather abstract the queries needed to get the data into the 'Infrastructure' layer?"
I cannot claim that this is a "Prism Ideal". Neither Prism nor PnP have taken a position on the Model component nor where to put persistence concerns.
I am a big proponent of keeping persistence details OUT of the view ... and the ViewModel/Presenter/Controller/PresentationManager or whatever part of a Separated Presentation pattern you prefer. I believe firmly in the Gateway and Repository abstractions ... as do many of my colleagues inside and outside IdeaBlade.
This perspective comes from our experience watching clients suffer as they scatter query and save logic all over the place. As the applications grow they lack consistency, lack exception handling, bloat with duplicated effort/code, exhibit limited opportunities for testing, ... the litany of trouble goes on.
The abstraction of persistence concerns is a UI recommendation independent of your client technology choice be it ASP, Windows Forms, WPF, Silverlight, the-next-great-thing.
As always, it is a matter of opinion ... strongly held by me in this case. I know you can succeed without following it. I just feel you'll be in better shape if you do follow it.