I do not believe you did an objectively wrong thing when discarding your human coworker"s concoction. However, it is a fact that you do not understand their culture, you admitted so yourself. It is therefore illogical to take any action regarding his lunch without his consent. In addition, humans are emotional creatures, and may not react favorably to your intrusions, no matter how logical they may be.
The logical thing to have done would have been to raise this issue to your coworker once you noticed it, taking with you your evidence that it would pose a health hazard to him and to the crew. Tossing it without his consent should be your last resort to protect the crew’s health.