So after all, 6x03 was pretty fruitless regarding valuable RJ clues.
The writers have been playing with us a bit concerning McAllister, twice avoiding height then saving PJ on the roof top. Then the bird scene, however with a totally normal reaction to a bird coming out of nowhere and flying into his face – no phobia implied here. (Also, he is calming down way to quickly for a phobic.)
The only real clue is McAllister pulling up PJ with his left hand. So we now know McAllister is left-handed. This does not make him RJ though ;)