It's hard to argue with some of your points but the spin of the story and the media has turned Embree's hiring into a witch hunt against Bohn.
What has Bohn done at CU: helped build the foundation including new facilities and a world-class coaching hire for a 19th ranked men's basketball team that has been a below average program throughout history, got CU into the Pac 12 just as conference realignment was about to explode, got the AD into the black, and improved several other athletic programs.
Let's talk the football program. Yes it is in terrible shape and it is/should be the cash cow and the hallmark of CU's athletic programs. But the solutions to improving the program include significantly increased donor support which at CU doesn't come easy.
His first hire, Dan Hawkins, was an absolute slam-dunk, home run, (insert any analogy you want here) according the whole sports world. He had one of the highest winningest percentages in college football and had led a previous perennial no-name mid-major into a BCS buster. Everyone in the sport praised the hire including all of the local media if I am not mistaken. It didn't work out, in part b/c in retrospect we learned the has OC at the time, Peterson, was actually the brains behind the operation.
Due to the state of finances at the time of his firing and the payout, and the clamouring from vocal Buff alum and supporters, Bohn was pushed into hiring Embree. A guy with undisputed passion for CU. Unfortunately, he was a terrible HC and maybe would have been good one day, but who wanted to wait around several more years to figure out if he could learn enough on the job to make CU competitive. But Embree presided over what is arguably the worst Buff team in history and one of the worst ever BCS teams too.
The Buffs were ranked 120th out of 120 teams in scoring defense and offense. The Buffs one one game this year by 1 point total while losing the rest of their games by an average of about 40 points. While Embree should had a right to assume he would likely get at least 3 years, noone could have predicted Embree would put that kind of product on the field. Not even Embree himself who had established getting to a bowl as the goal for this season. Embree is a great Buff but proved to be the wrong choice to bring CU football back to respectability.
Bohn is faced with a make or break decision with respect to Embree's replacement. If he gets this one wrong, he will probably be shown the door, but if not, his legacy will always be tarnished. But in light of his accomplishments during his tenure, I have faith he will get this right. The 3rd time's a charm.