It's not a question of morality, of right and wrong. It's just a question of being smart, of maximizing your value.
At the end of the day, Crabtree does need the 49ers more than the other way around. If they don't sign him, they'll move on with their franchise and they have 51 other guys who are willing to play and guys on their scout squad who would sign for the minimum. For Crabtree, though, playing in the NFL is far, far, far and away his best option to make money. I'm not going to denigrate that he's getting paid for just running fast and catching balls; plenty of people make more silly money for having less skills (you should see what I-Bankers make just for having a Rolodex of guys they've gone drinking with). But he doesn't have much in the way of outside options. If he doesn't sign, a number of bad things happen to him. First, he loses a year of playing in the NFL (anything can happen, but most likely). And it's not just a year of rookie pay that he loses, he'll still have to sign a rookie deal and then postpone his FA money so really he's losing a year of his most lucrative pay. Second, I would be shocked if he was drafted higher next year than this; signability issues is a real factor in the NFL and who wants to go through this with him again. So even his rookie money is going to be less than it was. Not to mention that the bloom may be off the rose a little bit, even signability issues aside... when Clarett showed up for the combine when he was actually eligible, he was a mess. Not saying that will definitely happen to Crabtree, but it could. He doesn't have much upside (he could only get drafted 6 spots higher) and he has significant downside (he could fall a full round or more).
And the 49ers don't have much incentive to move beyond where they're sitting. The NFL slotting system basically works (for teams). They're not going to get pummeled by their fan base any more than they already have been if they let Crabtree fall back into the pool and they could upset the apple cart that all NFL franchises rely on by setting a precedent of, "We won't pay you where we drafted you; we'll pay you where Mel Kiper would have drafted you."
Maybe Crabtree signs; maybe he doesn't; it's no skin off of my back. But I wouldn't think that he's a bad person for refusing to do so; just a kind of stupid one.