It would not shock me either way on Holt. I think a lot of his issues this season related to the vertigo and he did show some signs of life near the end of the season (September numbers were .256/.375/.708 in 24 games vs. .178/.275/.482 in 40 games before that). The September numbers to me are perfectly acceptable for a backup infielder plus he's relatively cheap and he can at least passably fill in in the outfield. That's a valuable trait in these days of 12 man pitching staffs.
Nunez provides much better offense and can handle infield duties, but after watching his adventures on pop-ups, I don't want him anywhere near the outfield. However, nobody knows how bad his knee is; it sure didn't look good.
Hernandez is a big question mark. Lin and Marrero are good infield defensive players but their minor league numbers show no offense.
Stay or go, Holt is hardly the main concern of the club right now. If he is, the Sox are in really good shape.