First off, it would make the front office look like a bunch of liars. Sure, all team executives fib and stretch the truth when dealing with the media, especially this time of year, but the 49ers have said, ad nauseam, that Alex Smith is their starting quarterback and that they believe in him and have confidence in him. Not only has York said that, but so have President of Player Personnel (and acting general manager) Trent Baalke and Head Coach Mike Singletary.
If all of a sudden they draft Clausen, then Smith, who's in the last year of his contract, will be a lame duck, knowing he has no future in San Francisco. Even though he'll be playing for the red and gold in 2010, in essence it would be the other 31 squads he'd be auditioning for in 2011 and beyond. Sure, technically the 49ers bigwigs can tell the media that they kept their word because it'll be Smith on the field and not Clausen, but that rationalization would be cheap and wouldn't appease anybody.
Not only would it be a bad decision from a public relations standpoint, but drafting Clausen would destroy Smith's confidence before the year even begins. All he's ever wanted was a chance to play for the same offense, with the same coordinator, two years in a row in order to establish some continuity. He's finally going to get that opportunity this year, but won't it feel awfully hollow if he knows his employers don't believe in him?
Drafting Clausen would not only hurt Smith, but it would hurt the rest of the 49ers in the short term as well. The rest of the NFC West is terrible. The Seattle Seahawks and St. Louis Rams are rebuilding. The defending division-champion Arizona Cardinals will try to make a go of it with Matt Leinart under center. The Niners, with just a couple of roster tweaks here and there, can not only win the division handily, but can position themselves to do damage in the playoffs when they get there. The team needs both of their first rounders (and likely their second and third round picks as well) to play immediately and contribute. They can't afford to waste one on a quarterback who'll be sitting on the bench next year.
Furthermore, I believe drafting Clausen would incite the fans. Why, they'll wonder, if you really didn't think Smith was the answer all along, did you not pursue a proven veteran like Donovan McNabb, who was on the trade market? If you're going to sell your current QB down the river, shouldn't it be for someone who you know is a definite upgrade? It would certainly send a mixed message.
Speaking of mixed messages, the final reason the 49ers would err in drafting Clausen would be the perception that York, a proud Notre Dame alum, got his way and that he's the one pulling the strings in the personnel department. Last month Scot McCloughan, the team's former general manager, left the team under mysterious circumstances and while York insisted that Baalke will be the chief decision-maker during the draft and that he had no desire to be the general manager, it sure would look suspicious if the 49ers ignored their pressing personnel needs, such as a right tackle, and risked alienating Smith, just to draft a quarterback in Clausen, who was below .500 in his three seasons for the Fighting Irish.
I'm not positive the 49ers will take Clausen if he's there, but I don't necessarily trust them not to take him either. Hopefully someone else – like the Oakland Raiders – will pick him first and take the decision out of their hands.