I don't think it's that, I think Sly and Puppeteer were never intended to release at less than full price, the market just forced Sony's hand, and I don't think that means Sony will continue that, they'll just not make games of that ilk.
I actually kind of disagree (and agree).
Sony, during the PS1, PS2, and now PS3 era, had a pricing strategy that priced their first party titles $10 less than current retail, which for PS1 and PS2 had them at $39.99.
When it comes to Sony, it seems like they are not adverse to making games like Sly or Puppeteer, even when they know that, sales wise, the games won't be doing CoD numbers. Games don't have to do CoD numbers if their budgets are managed properly, with realistic expectations, goals, and milestones.
I remember reading that Sony and Quantic Dream were expecting Heavy Rain to sell between 200,000 and 250,000 units. It went on to sell 2 million at $60. Far beyond their expectations.
I think they knew the market that Sly Cooper was releasing into, and priced it that way to, yes, push units, but I don't feel that it was just purely having their hand forced. They understand the realities of the current gaming market.