I don't want to answer for anyone else, but to me, the difference is the caliber of player. I think the argument is not that Nick's deal will cripple the team—it won't—but that it was a poor use of resources for a team in the Braves' situation, i.e. mid-payroll, rebuilding. From that point of view, the contract is a FA overpay for a guy who is probably untradeable, is possibly injured, and might very well be a boat anchor by the end of the deal.
So you're arguing that it's a better relative value over time. Sure, but that's like saying that you got a really good deal on a car loan, and purchased a high-mileage vehicle with low resale value and questionable reliability.
disclaimer: I like Nick Markakis and hope that he rakes, plays GG defense, and polices the clubhouse as promised.
Which I do think can be said of just about all free-agent contracts, regardless of the caliber of player. Just about every contract we've seen in recent years have typically been described as being 1-2 years too long, a million or two too high, etc.. That's what happens when bidding wars start, and the team that's willing to eat the most during those last years usually wind up getting the player. That's just the cost of doing business in the free-agent era.
I've always agreed with those who said it was an overpay, but they wanted the player (for whatever reason - there's no need to re-hash those arguments) and that's what it took to get him. Someone mentioned earlier that what we can only assume is that they expect him to be able to help the young players adjust and that that will offset a portion of the eventual declining performance by helping them outperform their contracts.
FWIW, they had Pendleton around for his "presence and leadership" when he put up an OPS+ of 91 in 1993 and 73 in 1994 and those teams didn't turn out too bad.