"Mit den Jungen isst das Mädchen."
Because of the cases. It's "mit den Jungen", not "mit dem Mädchen". If it was the other way around like you suggested, the sentence would be: Mit dem Mädchen isst die Jungen" Although I am not positive if I spelled jungen write in this case...
You're right. But in your last translation, it has to be 'essen die Jungen', since they are 3rd p. pl. :) To make this sentence much clearer, one would usually say: Das Mädchen isst mit den Jungen. 'the boys eat with the girl' would then be: Die Jungen essen mit dem Mädchen.