Analyzing the קִיְּמוּ וְקִבְּלוּ episode. If it is actually a valid complaint, why were the Jews punished for sins in the Biblical Era?

Analyzing the קִיְּמוּ וְקִבְּלוּ episode. If it is actually a valid complaint, why were the Jews punished for sins in the Biblical Era? — מובחר ועד הנגינה