They were stupid to give the developers an out. It's not hard to do some math and figure out what it would take to recoup the penalty in rent or sales compared to the much lower revenue stream of affordable housing.
Now the fine is just part of the cost of doing business. They'll either eat the fine, or more likely spread it out across whatever they were gonna charge for whatever they're building instead of the affordable housing.
You can't give greedy assholes an inch, or they'll take a mile and then bill you for it.