Honestly, it is too easy to hit the gunner with splash. During WFA's early betas, she wasn't locked to the floor. You could actually bounce her in the air and she'd stop firing because of the ground check. We had to lock her to the floor because marines would totally destroy her by bouncing her around because she couldn't move.
What you propose is to let her keep firing, but bounce her around even more because of backwards push from firing the mega. I think you'd still end up with a situation where it would be way too hard to aim as a gunner and you'd be flying all over the place from bounce push.