I agree that Diana either knows exactly what happened or has a pretty good idea. And she is trying to keep it from Reid. She doesn't want him to find out what it is. (And that may be why she doesn't like the idea of him working on cases involving young children.)

She slipped up in that conversation she has with Spencer. At first she tells Reid that Riley was just a story he made up. After Reid tells her he's been having dreams about Riley or finding his body she tells him "you always were a reader - it effected your dreams" So she might have known that Riley was real and little Spencer had read about his death/murder.