gameplay wise, you can't fault the devs for their choice. having to be on foot, or un armored would make ejecting a penalty, as opposed to saving your life. immagine having to run back to base at half the speed of a sprinting BA. that would take damn near the whole game. having a BA makes returning to base actually doable, and makes ejecting having a purpose.
the issue comes from fully kitted out BAs ejecting, and having alot of firepower. simply make a fully outfitted BA, similar in cost to vehicles and some of the lighter mech classeslike a 20-40k range. that way if they want to have a BA with alot of hitting power, they have to sacrifice vehicle/mech strength. right now they have their cake and eat it too. they need to make a choice, either a heavy hitting BA setup, and cheaper mech/tank, or a more expensive mech/tank, and little BA effectivness.
this would be the simplest way to change it imo, and would require minimal coding outside of tweaking cost numbers, and would balance everything out.