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Initially, as Simon stumbles out of the trees to deliver the "good news", the boys think he is the beast. The tragic irony gets worse as they stab him about 300 times. THe boys were in a frenzy when they killed Simon and I do believe many of them knew exactly who they were killing. Simon was a "Christ figure" and had to be killed by his own people. By this time the boys act as one blood thirsty animal rather than individual boys with the normal faculties of perception. THe irony of thinking their saviour was the beast is not lost on the reader.
The boys are in a frenzy, they're dancing and chanting. Simon's emergence from the forest is taken as the appearance of the beast, that's what they initially believe they're surrounding. Do they know it's Simon? Maybe not at the beginning, but yes, they know.
Just to elaborate, I think the boys knew exactly who they were killing. It is even alluded to that Piggy, Simon and the twins may have been part of it. The killing frenzy was just so strong.