In the first book, it's said that it was Tywin Lannister that sent Thorne to the Wall. Although the Starks did support Robert's Rebellion so that could indeed be a large part of Thorne's hatred for Jon. To quote from the book:
"Chip the ice off your eyes, my good lords. Ser Alliser Thorne should be mucking out your stables, not drilling your young warriors."
"The Watch has no shortage of stableboys," Lord Mormont grumbled. "That seems to be all they send us these days. Stableboys and sneak thieves and rapers. Ser Alliser is an anointed knight, one of the few to take the black since I have been Lord Commander. He fought bravely at King's Landing."
"On the wrong side," Ser Jaremy Rykker commented dryly. "I ought to know, I was there on the battlements beside him. Tywin Lannister gave us a splendid choice. Take the black, or see our heads on spikes before evenfall. No offense intended, Tyrion."
It's also notable that Thorne immediately befriended Janos Slynt when he arrived at the Wall, even though you'd think that with Thorne's elitist outlook he would sneer at someone like Slynt who many of the nobles considered to be a commoner who jumped above his station. Slynt was exiled from King's Landing by Tyrion Lannister, son of the man who exiled Thorne, for political reasons.
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