The Royals are saying this is a financial decision, since Pena is under club control for another season and the Q would have been a free agent at year's end.
It's also a smart baseball move, as Pena is a switch hitter and so far this season has put up better numbers than Quintero (268/295/358 vs. 232/257/34).
Personally, though, I would like to think this speaks to a larger truth: that the Royals are continuing to build a great baseball team. And that after talent (which trumps all else), attitude matters. Because, at the end of the day, now that Salvy Perez is back behind the plate, it doesn't much matter who's chatting up Bruce Chen during his starts and riding the pine the rest of the time.
But, Brayan Pena loves the Royals. He has said so for longer than people may realize. He WANTS to be here, and has expressed a willingness in the past to sign for below market value to stay. He's the kind of role player you want to reward for his loyalty, because it makes guys like Perez, Alcides Escobar and Alex Gordon feel good about their decisions to sign long-term deals.
At the end of the day, the Royals will never win a bidding war for the big guns in free agency. But, when guys like Zach Grienke come onto the market, and they aren't looking for just big money, but also a good environment, keeping people like Pena around may add more value than just their on-field contributions.