Is it unethical to remove another plugin’s meta keys?

I don’t see anything unethical in this… There are many plugins that remove some data from DB as part of their optimization process.

Also there are plugins for some migrations (like qTranslate -> WPML and similar). They also can remove data of previous plugin after migration is done.

The only thing I would be very careful is to make sure that users know, what exactly your plugin is doing and that the data will be lost. Maybe even put it as an option, so that user decides that he want to delete these meta values.

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