I really doubt Thornton signs at 4 million per year or less. I would think it would be somewhere closer to 5, although the injury certainly muddies this estimate. If I'm right on those figures, I'd let him walk. 2 years 9 mil is about as high as I'd go. Real question though, if you are Thornton, why do you want to resign with San Jose? Barring anything drastic, Edmonton, Anaheim, and Calgary are clearly above San Jose heading into next season in the Pacific. Nashville, Chicago, and at least one of Minnesota, St. Louis, and Dallas are likely above them in the Central. I just do not see a clear path to winning a Cup here.
Regarding Marleau, his market will certainly not be as bullish as Thornton's, so signing closer to 4 mil feels more plausible. Would you give him a 3rd year and see if he takes less per year? He should be good for around 15-25 goals (depending on PP time), and 35-40 points. Those are slightly better than Joel Ward numbers who currently makes 3 mil. Factoring in inflation, and you get somewhere around 3.5-4.5 (tops) per year. I'd welcome him back at the low end of that range. Also, regarding his market, it seems as though it's essentially limited to the California teams plus the Rangers, which in theory should help San Jose if they want him back.
As others have suggested, I'd certainly explore kicking the tires on moving Pavelski. You can already see his game slowing down, and after having one of the more cush jobs in the NHL as JT's right hand man, I think we've clearly seen his apex. For all the talk of him being this playoff warrior, he has gone through long stretches where he invisible yet never really gets called on it (as opposed to say Marleau). Marc Bergevin likes to make stupid trades, if he offers Galchenyuk and perhaps a pick for Pavelski, don't you have to do that if you are the San Jose?
I'm not sure if San Jose can get a better season from Schlemko than the one they just received, but I am 100% on board with jettisoning Martin and giving his minutes to Schlemko. Ideally Ryan or Demelo would be a cheap option on the bottom pairing.
I'd also really consider moving Hertl. His injury history scares the **** out of me, and his production away from Thornton just has not been there. I thought his playoff performance was pretty underwhelming, but obviously you have to factor in the injury. At best I see him as a high end second line player, who you can never depend on to stay healthy. I fear his career goes the way of Michalek -- good but not great -- and if you can him now for a strong return, you are better off for it.