The Empire was eventually defeated, but they was able to sue for peace. The top brass of enemy countries, due to the massive loss of life on all sides, considered the offer but also realized that Mary Sue, would accept nothing less than the Empire's complete annihilation (she wanted to commit genocide on the Empire for killing her father, not just Tanya). Fearing disruptions to the peace talks, the order for Mary's death was handed down. In the end, she was tricked and betrayed by her own comrades, who secretly hated her for her naivete and recklessness, and cruelly stabbed and cut literally to pieces. One of her former comrades said Mary Sue will never be remembered and her death was a dishonorable discharge.
TL;DR: Mary Sue got the Caesar treatment.