yekke2 –
There are two things to consider.
1) The Rambam’s shita isn’t uniquely his – it is simply a machlokes in the Gemara and he is “paskening” like Shmuel. So no Midrash can really be a kashya, because Shmuel can disagree with it (????? ??”? that the Rambam himself cannot, which is not entirely a valid argument itself).
2) All of the things you cited can easily be interpreted allegorically, or in ways similar to Wolf’s mehalech above. For example:
Yetzer hara being abolished: Since knowledge of the truth will be so clear, people pashut won’t have any yetzer hara to do what’s wrong.
Pig being kosher: Scientists will figure out how to genetically alter the pig so that it chews its cud. (See Ohr Hachayim in Shemini by the four animals, where he brings down this Midrash.)
Lions and lambs living together: An allegory to the lions and lambs of the world. Meaning that people will stop fighting with each other.