I don't recall how much time Bekele had between the 10 and 5 in Paris, but he had quite a lot of time between the 10 and 5 in Athens, and he actually got in some significant workouts during that interim period. Also, his Paris 10K was probably a somewhat harder race than his Athens 10K, with a second half that was significantly under 13 flat.
In contrast, El G had almost no time between a very hard 1500 against Lagat and the start of the 5K competition in Athens. I would have expected El G to be more fatigued than Bekele going into the 5K.
Of course, none of us knows why Bekele did what he did in the Athens 5K, or what he was feeling on the day of the race. But I've never heard a good explanation for his choices in that race, and I've wondered if he simply overestimated his ability to outkick El G if he got the jump on him with 300-400 meters to go.