Mewtwo won't create a Bad Egg. Don't worry. :)
The only way Bad Eggs are created is by hacking them into the game yourself, and the result of the Pokemon you were trying to create may become a Bad Egg and ruin your game. Bad Eggs are there to protect your game from the dangers of hackology. :D :D :D
If the Mewtwo isn't a Bad Egg now, it will never be a Bad Egg. Of course, you can do anything in hacking, but you got in a trade. So if the Mewtwo isn't a Bad Egg now, it will never produce any. :)
Hope I helped. :)
Source: Experience