And she simply wanted to use Yuri’s unorthodox interests and awkwardness to make her seem unappealing. Sayori and Yuri die as a side effect of Monika tampering with them – she originally wanted Sayori’s depression to simply prevent her from confessing to the MC in the first place, out of fear of rejection.
So, in a desperate bid to try and rescue the happy ending she tried to give you, she attacked Sayori. Monika recognized that you, the Player, deleted her likely for ALL the other girls, not just Sayori.
You might be interested: Question: Rules Of Literature? Why did Monika kill sayori?