These Dale Jr. conspiracy theories have been popular for a long time, although they're not as prominent these days since Jr. hasn't exactly appeared to benefit from any special favors the last few seasons. But I don't buy it, either in this specific case or in general.
Jr. has always been good at plate tracks - he qualified second last year. He had a late spot in qualifying this year, which means all of those previous guys would have had to guess how fast Jr. would run and then run just an infinitesimal bit slower. Guys trying to make a name for themselves like Trevor Bayne and Paul Menard would have had to willingly give up their shot at a little bit of publicity.
Beyond that, there's just too much money and ego and competitive drive for sentimentality like this to just fly below the radar. You think Jack Roush would willingly let a Hendrick car beat him for the pole? You think the Busch brothers, Hamlin, Biffle, Happy Harvick wouldn't speak their minds if they had even an inkling of such a thing?
And as for NASCAR themselves, the very last thing they need in a time of sinking ratings is to risk a huge scandal over deliberate competitive favoritism. They're not going to gamble their multi-billion dollar brand on a group of probably underpaid tech inspectors going along with cheating and permanently keeping their mouths shut. And anyway, if they really wanted to do something to boost ratings, they'd fill Jimmy Johnson's frame rails with lead
As for the race itself, I could see Jeff Gordon maybe trying to help Jr. lead lap 3, but that's about all the favors he might get. I'm sure if you asked the other 42 drivers who they'd want to win besides themselves, Jr. would be a popular choice, but they'd all 100 times rather it be them.