The biggest thing is being aware of the respective targets from the get-go.
Decide what your 'Wing is going to blast, and figure the typical threat-zone of the scattering missiles... then simply don't put your trueborn there. I mean, they can DS perfectly anywhere on the board, yeah? Unless you're playing on a 2x2 area, I would hope there's a safe place to land them out of the danger zone!
In theory, even if you are planning to use the Trueborn to open up a transport, and the Fighter to boom the contents after, the 'Born have an 18" range... utilize it. Only the nip of the boat has to be within 18" for them all to fire at the nip of the enemy vehicle... even if the unit disembarks directly toward the Trueborn, the blasts would have to basically scatter full distance directly at them to hit... so any risk there is pretty legitimately minimal.
Of course, this is all dependent on the board layout and location of enemies, etc, but keep these things in mind next time, see if it helps.