Personally I don't think that the behaviour is the main problem, it is will hardly hurt the prublic image of Trek as only fans are aware of it. But I think the nutty conspiracy thinking does influence Orci's writing and I think that he will be a worse director than Abrams. Frakes did at least direct some TNG episodes before he directed two movies. On the other hand Orci has production experience.
I think it is a pity that Abrams will not direct the next Trek movie. I might not like his way of story-telling but from a technical perspective he is undoubtedly one of the best directors in Hollywood right now; Trek made a visual warp jump under his direction.