I have no good knowledge of neuroscience, so I'll be happy to read other thoughts on this. Personally, it seems to me that this is an evolved technique to direct us to:
act on impulses at the moment of an event, instead of contemplating rational choices that may take too much time to arrive at (thus limiting our chances of survival);
pursue rational choices in calmer times, trusting us to draw on stored memories of similar events to help make better decisions (the purpose of Deja Vu?)
For the link between the hippocampus and the cortex being required to retrieve memories; maybe those memories are useless without the emotional context, and the hippocampus is needed to relive those emotions to have a more accurate recollection of the memories.
It might not make sense (I know almost nothing about neuroscience), but it's a thought.