A few things:
1.) Of course Wilforl would make more money this year, possibly double the franchise tender amount or more if he signed a long term deal. That doesn't make the franchise tender money an insult. It is good money just not as good of money of a long term deal would provide.
2.) If history follows suit, Wilfork will benefit financially long term if he is franchised this year and able to get a long term deal next year barring injury. Look at Asante Samuel. He played for one year here under the franchise tender which was I think $7-8 million. The next year he got as good or better deal with the Eagles than he would have gotten the year he was franchised. Odds are that he wouldn't have gotten that $7-8 million that he got during the franchise year on the back end of his contract if he got a new deal right away is neglible. You go back and look at other franchised players like Nate Clements, Orlando Pace, Walter Jones, and so on and the trend shows those players made far more money than they would have if they reach free agency right away. There are exceptions, but most make more.
If Wilfork is franchised and is forced to play out this season for $7 million, the risk is that he gets injured and loses out in a new deal next year and the reward is that if he has another great year he will end up making more money in his career. There are upsides of being franchised.
3.) As for Wilfork being underpaid, that is relative. Was he underpaid based on his value? Yes. Was he underpaid based on the contract he was given and his value at the time he signed it? Absolutely not. Many players quickly outplay their contract, especially rookies. Very few get to get the value increased more than a year before their contract runs out. I guess the Pats could follow the Eagles' model and renegotiate with young players two years into their rookie deals, but we have seen that open a whole other can of worms where these players get above market value deals and continue to improve and then want to renegotiate again after a year or two. The Cards got in trouble this way with Boldin too.
4.) I'd like to see the Pats lock Wilfork up for at least 3-4 years (longer could be a risk based on his age, position, and size). I think he deserves a contract that is among the top DTs in the league (although not as much as Haynesworth because that was a ridiculously stupid contract at $12 million a year for four years). But we do not know what the Pats are willing to offer nor what Wilfork is asking for. If Wilfork's demands are in the Haynesworth level, I say that the Pats stick with the franchise tag and gamble on the future.
If Wilfork is going to get $12-15 million a year and Brady possibly getting upwards to $20 million a year (if Eli Manning can get $16 million a year and Peyton could drive that number up too if he gets a deal first, that is the number we could be looking at for Brady), I don't know how this team will field a winner especially if the owners get even half of what they ask for and there is a cap consolidation. Based on the numbers I saw that if the owners get back 18% of the revenue from the players, the cap could shrink to under $110 million where Brady and Wilfork could account on any given year upwards to 32% of the cap.
From my standpoint, this is not an open and shut case of paying Wilfork whatever he wants. There are far too many variables that could kill this team. This is why the Pats have been so cautious about making long term deals and why they are not even going to think about negotiating with Wilfork until a week or two. A new CBA could cause what we saw in the mid-90s where dynasties like the Cowboys and 49ers got gutted because of the cap (even with the 49ers cheating the cap).