After watching episode 6x03 I don't think we have more reasons to suspect McAllister than we did before. What did or said doesn't prove anything. we can say he's RJ because we can see everything we know (or we are made to beleave we know) about RJ to discribe this guy!
Well no. We have not made any progress if everything he does or say can be also explained in a logical way. Why. Because then it's up to Heller to deside if he is RJ and make it happen.
Only things that could not be explained in other way than him being RJ, can be taken into account. Why? Because we have strange things for every other person in the show, that could be explained with that person being RJ.
So. What did McAllister did in this episode? CBI arrives at his jurisdiction and takes over.
The same happened in episode 1x02 and he was not happy about it, although he wasn't showing it much. Then he got emparased with Van Pelt and he didn't solve the case, Jane did.
So we expect him this time to be polite, cool, cooperative and not get in their way in a way they would get offended.
At the same time he has to show any way he can that he is sheriff for a reason and he isn't useless. And we all see that he does more than that in the end.

OK in the chapel Lisbon tells him to climb the ladder to get a hammer. Well nice is nice but he wouldn't do labor for these guys, he can get others to do work. So when he says about he would need other shoes, it's obvious that he is in the sheriff's shoes, and their errand boy. Look at the that scene. Can you see him standing like the authority he is?
Later at the cliff Jane tells him "come over here fela have a look". Well he is no "fela" he's the sheriff! Doesn't mean he's suspecious that he didn't go. And don't forget thet he was interupted.
From then on he is the nicest guy really. When Jane tells him he and his men need to hang back while Jane puts his plan to work, McAllister has no problem at all.
After he saves Jane he finaly tells him that he ignored him telling him to hang back, because he didn't trust them the way they forced their way to this case. He is still polite though. As for the pingeons flying to his face, well no one would like that.

Personaly I don't see anything suspicious about McAllister in this episode.