Just stay away from the league leaders in the mega Ks then don't sweat it too much. Ks are hard to predict. I was in a league last year that counted offensive Ks and I tried to pick up guys that had low K totals...I ended up as one of the worst teams in Ks.
Many of the same players you question the skill of now...
Dunn, Soriano, Sosa, MacPherson, Sexson, Cameron, Branyon, etc.
Thome is an interesting exception to this. He Ks a lot, always has. But he walks a lot also (good OBP) an he obviously puts up great 5x5 numbers. If you league also counts walks, their is a good chance that the walks and Ks cancel each other out to a great extent.