This is purely hand-waving, but one scenario where natural selection loses the gene is where the expression of the NIN gene created a vulnerability for a virus/

This is purely hand-waving, but one scenario where natural selection loses the gene is where the expression of the NIN gene created a vulnerability for a virus/bacteria/fungi that would kill out the plant. Considering the gene involves a pathway that hosts symbiotic relationships with micro-organisms, it seems possible. In such a scenario, the only surviving, reproducing individuals would have mutated in such a way to suppress expression of the gene. (Again, there is no evidence of this, it's just conjecture)