It didn't happen, but it the position was offered, a contract was written, and the details were in negotiation. The nail in the coffin was the bowl game. It was also one of the least intelligent ultimatums I have ever heard due to the timing...Perkins wanted him in Lawrence to assemble his staff and to start recruiting...but the dead period started on 12/17 (Gill hired on 12/14) and ended on 1/11 (Sun Bowl was 12/31). Harbaugh had more than enough time to hire his staff and get set up before the dead period ended (Gill was still hiring staff in January IIRC) and 3 days worth of recruiting doesn't mean squat.
Anyone that is calling BS needs to take a step back and evaluate the state of the two programs in 2009. If you are trying to look at the two programs from a 2015 perspective, it's a no-brainer. In 2009 though it was a much, much different story.
Stanford circa 2009: Stanford's football stadium went through a $100 mil renovation in 05-06. Stadiums are typically renovated for benefit of fans, while locker rooms, weight rooms, and offices are renovated for the benefit of the players. It decreased capacity from 85k to 50k. The 2009 team was the first Stanford team to go to a bowl since 2001. Stanford's avg attendance in 2009 was 41435 but was skewed by hosting ND and Cal for The Big Game (both were above capacity). Avg attendance for the other 5 home games was 37805. They had a new stadium that they couldn't fill up in their first bowl season in 8 years. Harbaugh was making $750k and his contract extension and negotiations had been stalled for a year because Stanford didn't want to give the impression that athletics were more important than academics. The general opinion at that time was Harbaugh didn't deserve a raise because he was already making twice as much as the university president.
KU circa 2009: $31 mil football locker room, weight room, football office facility was less than 18 months old. Attendance (home games only, not counting Arrowhead) in a 5-7 campaign was 50586 with only one game falling below 50k all season. KU had been bowl eligible 4 of the previous 5 seasons. Mangino was making $2.3 mil in 2009 and the administration had shown a history of stepping up when it came to coaching pay.
Harbaugh was NEVER going to be at Stanford long term. He was always shooting for the NFL and it was a always just a matter of how soon it happened. Knowing that, it was about piling up wins and making money. At Stanford he had 9 conference games and 3 noncons...one of which is always Notre Dame. Remember we're talking about 2009 here. At KU, he had 4 noncons with the freedom to schedule whoever he wanted to include FCS teams. He also had a relatively soft 5 game Big 12 North slate. Then he had a 2 year set with Okie St/Baylor/A&M or OU/UT/Tech. That's a recipe for 8 wins in most years and 10+ in good years for a good coach.
The contract Gill got was Harbaugh's with some tweaks. So Harbaugh was offered 2 mil a year for 5 years with a full contract buyout. That kind of contract makes sense for an up and coming coach who had already interviewed for an NFL gig (Jets January 2009) who would also likely be on every Muchigan shortlist for eternity as long as he performed.
If you're looking for evidence that Harbaugh to KU look at the contract that Gill got. A guy making 400k with a .400 record at a non-AQ school who had only been interviewed by one other program (Auburn 2008). That resume doesn't require increasing a salary by 5 times nor does it require the same type of buyout.
I hear what people are saying about just trying to force an extension/raise at Stanford. That said, guys that are trying to get a raise don't turn down 2 mil to make 1.5 mil...especially guys that know they aren't planning on being there any longer than they have to.