It's not about what WP Engine could have done, but how Matt acted. If he wanted WPE to use their own Plugin repository, he could have told them so and given them a date. But cutting off access to updates without warning to all these sites is inexcusable. Matt chose the "nuclear option" without realizing that the fallout would also hit WordPress and himself. In addition to hundreds of thousands of websites that had nothing to do with his gripes.