Structure & Tone
The story starts with a lighthearted, fitting tone for the MLP universe but takes an extremely dark turn that feels jarring given the source material. While it's okay to write darker themes, the shift from making cheese recipes to cannibalism is too extreme and doesn't align with the show's core values or target audience.
Character Consistency
Twilight's decision to exile Pinkie and Cheese feels out of character. As the Princess of Friendship who values rational thinking, she would more likely investigate the incident and seek a solution.
The extreme reaction to Rainbow Dash's allergic reaction also seems disproportionate. The MLP universe typically handles conflicts through understanding and reconciliation.
Alternative Suggestions
Consider reworking the conflict in a way that maintains the show's spirit while still creating drama:
Instead of exile and death, perhaps Cheese and Pinkie could go on a journey to find a cure for pegasus cheese allergies
The conflict could focus on Cheese learning to adapt her recipes to be inclusive of all pony types
The story could explore themes of friendship and understanding through cooking mishaps without the extreme consequences
The Ending
Rather than the current dark ending, consider a resolution that teaches valuable lessons about:
Food safety and being mindful of others' dietary needs
The importance of communication
How mistakes can lead to growth and understanding