Orc blood IS a racial bonus, as is elf blood for Half-Elves, and I assume these racial bonuses were taken in to account when balancing the races. We are just arguing what that means.
Applying the halfling +1 attack bonus directly to this debate is not my logic, it is yours. I don't feel the halfling attack bonus to thrown weapons is directly analogous to this situation. However, since you brought it up, it again emphasizes that the halflings are good at throwing a particular kind of STONE, hence they have a bonus at all thrown weapons. The stone in reference is the halfling skip-rock. It makes sense that, if they grew up throwing the skip-rocks around, and they have an attack bonus when throwing because of their familiarity with throwing that stone, that they should also be proficienct with the skip-rocks.
You tell me. Why would halflings be NOT proficienct with throwing those stones, if they get a +1 bonus to throwing anything because of their extensive experience with them?