My thoughts are this, he should of known of the clause, he did sign the deal, and if you dont read it yourself, your a moron. The only way he gets the $2M back is if he agrees to a team friendly long term contract. I don't think the 49ers have any responsibility to him. It's harsh, but it's the truth.
Now, if he would take a Carlos Rogers deal, he would be worth it. But if he is looking for a big pay day, like Finnegan(STL) and Carr(DAL) got, he wont get it here. The market wont dictate it. Of course it takes 1 team to do so. But with the cap flat, teams are being more cautious about deals. If he would take a 5yr $33M deal, thats $6.6M a yr average, I say do it. I would love to see Brown and Culliver start for the future at CB, with rooks drafted high to be 3rd and 4th CB. Cut Rogers when time is right.
The thing I would consider if I was Baalke, is trading Rogers, get as much for him, also that $1.25M guarantee he got then goes to the trading team who acquires him. It would result in an extra $1.25M savings. And he would save between $10-$11M over 2 years, with little dead money. Imagine that being used for Kap, Aldon and Iupati.
I hope and plan on doing a podcast on the salary cap for NinersNation.com. So when time comes maybe I can set up a twitter feed to ask certain questions.