When he was signed, he was coming off back-to-back Pro Bowls and had been tendered the year before. Typically when a player plays underneath the tender, you essentially sign them at FA market prices the next year because you've lost most of your leverage on them.
Also keep in mind that prices are depressed this year. In 2011 the top FA Safety was Eric Weddle, and he got a 5 year $40 million dollar deal, as opposed to Harpers 4 year $28 million dollar deal. Dawan Landry, who was slotted behind Harper in terms of "free agent desirability" went for 5 years / $28 million.
We definitely didn't get a discount, but we did pay market value for him. And I think everyone on this forum was on board with it too.
It was the 49ers game to end 2011 and the Spags disaster of 2012 that's exposed his deficiencies so glaringly.