Multiple sources are confirming that the San Francisco Giants and starting pitcher Tim Lincecum have verbally come to terms on a two year contract extension worth between $40 million and $41 million. As a Super Two, the deal takes care of Lincecum’s third and fourth years of arbitration, but fails to lock up the ace for any of his free agent years.

Considering Matt Cain’s impending free agent status after 2012, a failure to lock up Lincecum beyond his free agent years will most likely be seen as a bad thing by the arm chair GM set . . . but slow your roll, pilgrim. There are a couple of factors making this contract a very smart decision by Brian Sabean and the San Francisco front office.

First of all, there is a difference between Tim Lincecum over the last four years and Tim Lincecum over the last two years that simply can’t be ignored. If we look at his collected numbers since the beginning of 2008, we see one of the best pitchers in the league (fifth best according to fWAR), but if we look at his numbers since the beginning of 2010, we only see a very, very good pitcher (12th best according to fWAR). That’s not a slight against Lincecum, if anything it’s a credit to what he did in the 2008 and 2009 seasons when he won back to back Cy Young Awards in only the second and third seasons of his career.

As a pitcher, Lincecum has shown a tremendous ability to adapt to how batters read him, trusting more in his curve ball in 2009, introducing a two-seamer in 201o, and last season relying more on a harder thrown slider than he has at any point in his career. However, the difference in approach hasn’t always had the best results with a declining strikeout rate and ascending walk rate in each of the last two seasons.

It’s very unlikely that the Giants would be getting a discount by paying for the pitcher’s first or second year of free agency right now. In fact, they’d be paying a premium with his two Cy Young Awards still looming in the not too far distance.

Secondly, with the structure of the Giants payroll the way it is, the organization can afford to wait and see exactly what Lincecum they’ll be getting for 2014 and beyond. As it stands right now, by the time the 27 year old’s current deal ends, San Francisco will only be committed to a single contract, that of Pablo Sandoval’s, and at a very team friendly cost of $8.25 million. Their most likely best position player, Buster Posey, will only be reaching his second year of arbitration, as their best young pitcher Madison Bumgarner most likely reaches his first.

Of course, things will change in the next two years, and contracts will be added, but none as oppressive as Barry Zito’s, Aaron Rowand’s, or even Aubrey Huff’s. With the two year deal in place, a worst case scenario will result in either: 1) the Giants overpaying for a dead armed Lincecum for the next two years, or 2) San Francisco, like every other team in baseball, having to bid on the free agent services of a revitalized Lincecum, returned to his former Cy Young glory.

Neither of those scenarios are all that awful. In the first case, the Giants would only be on the hook for two bad years of Lincecum, which after the length for which Barry Zito has been a part of this team, should seem like a weekend. In the second, as I outlined above, the Giants payroll should be in a place where they can afford to pay a premium for a great pitcher of Lincecum’s ilk.

We tend to criticize San Francisco’s front office a lot up here, suggesting that their success in recent years has been accomplished in spite of their transactions rather than because of it. And while they way that they’ve handled the Lincecum deal in no way makes up for some other curious things they’ve done this off season, they have done well to not ┬áinterfere with a future that’s well set for a type of fiscal success that will transfer onto the field as well.