Note you should not disable bone transform inheritance for IK with 2 bones. 2 bone IK does not support that, as soon as you disable inherit transform the IK constraint will no longer be applied. This will show a warning in the new Problems view in 4.3.
If your parent bone is using 1 bone IK and the child bone is not constrained by IK, then that is OK, you can disable inherit transform on the child bone (or parent bone, 1 bone IK supports that).
Aiming with an IK bone is common. You don't need to disable inherit transform to do that. I think it's a bit strange to use the child IK bone as the projectile. Usually you would spawn a new object and use that as the projectile. You'd give it a vector and move it in that direction each frame. This way you could shoot many times and have projectiles all traveling in different directions.
If you do want to use the child bone as the projectile, you would set the rotation in code so when you disable inherit transform it remains pointing in the same direction. Is that what you want to do?
