Oh, I totally agree with you. NFL players used to play for far lower contracts (not only in absolute dollars, but also relative to the rest of the economy) than they do now, so I find it extremely hard to believe that many players faced with the prospect of millions would truly take the drastic step of sitting out an entire season, no matter how hardball GMs played. Even if they did, they'd not only lose out on the opportunity cost of a protracted holdout, they'd probably find themselves blackballed in the league and thereby lose out on real dollars if they were signed by another team the following year.
I think what NFL GMs are trying to forestall is a) the perception that they don't run player-friendly teams; b) creating disgruntled players who try to renegotiate their contracts at the first opportunity; and c) the public-relations backlash that ensues when such player difficulties arise. The problem is that situations b) and c) occur anyway, so what are they really afraid of? I think by throwing meat to the wolves, they're actually making them bolder.
The rookie slotting system, while needed, is realistically just a crutch for their lack of backbone.