Its not that she was killed becoz she did wrong things. She was killed becoz she was royalty. Of the fallen country.
SPOILER
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Part of the reason she was executed in the original timeline was due to a conspiracy. There's an anarchist organization called the Chaos Serpent whose mission is to destabalize governments. They did a bunch of terrible things behind the scenes (like murdering Tiona's dad) and blamed it on the imperial family. So in addition to being incompetent rulers who over taxed the poor, Mia and her dad also were executed for additional crimes they didn't actually commit.
We get to see flashes from the original timeline and later on in their lives in that timeline, both Tiona and Sion regret executing Mia.
I feel that Mia being executed was a bit much. Most of the things she was being accused for was while she was at school and how could she as a kid stop an epidemic, know to help the broke Nobel girl of the street etc. Yes she was an ignorant brat but she wasn't evil and not once does it show that she wished for the country's downfall. And why is a prince in a different country being so innately involved in the country's affairs. I frankly dislike the crown prince because in his 'perfection' so far he just selfishly acts and I prefer Abel. But anywho I stan Mia trying to not die and I really hope that Abel is ML.