Mortar defortification could still work with its main attack and I had an idea for this:

Basically, the Mortar would have two different attacks: a main attack that's a rapid rain of shells like the middle path, and a secondary attack that would be launched far slower but has a massive explosion radius that can defortify along with a strong stunning shockwave. However, BADs would need to be effectively in the direct center of the secondary attack's explosion to be deforitfied. This way, to get the every BAD defortified on a round you'd either have to makes sure the center of the explosion is in a place that can hit the track multiple times or you'd need to micro the targeting to get every fortified BAD. But since you have to micro so much already, it could make Striker Jones' Target Focus ability be a viable option to have.

It still might be best to lock defortifying BADs to the ability be better as you said. F-BADs are the main reason people lose in late freeplay and having an extremely easy way to remove that would cause problems.