I don't think so. What you are seeing is what you are getting. They are playing JJ to give him experience but there is no secret plan to give him the job unless/until McNamara starts to fail in more ways than he is failing now - which could of course happen. But I think the fans and media are projecting the play some of some of our really bad previous QB (like Patterson) onto McNamara. There is a difference. Despite the deep misses, McNamara makes a lot of good throws around the rest of the field and that coupled with a low turn-over number is worth more IMO than the talking heads give it credit. The truth is as long as the O moves the ball, you only have to throw the deep ball to keep the D honest - you don't need to complete them as long as you can continue to get 1st downs, and the M offense has been able to do that. We all assume it's going to get more difficult, but it has to play out.
So we are likely to see how much Harbaugh really channels Bo. Bo would lose before he let game conditions dictate his choice of players and given the way Harbaugh stuck with a Patterson who was far less effective than NcNamara makes me think Harbaugh takes the same approach.
Not saying I'm a fan in any of this, but that's my guess about it.
And of course the worst possible outcome is that the outside pressure gets to either Harbaugh or McNamara and they start trying to force throws that result in INTs.