I don't think he will end up boxing, Dana White, the Fertita brothers, and the rest of the collective ZUFFA brass are no fools. Regardless of peoples opinions of him, they know people will pay money to see him fight, and I don't see them blowing that opportunity. They recognize that his stock is high right now, and they'll find a way to work it out.
I personally believe they're just using the boxing claus in his current contract as a bit of leverage with ZUFFA. They know it's going to be hard convincing ZUFFA to pay Nick $175,000 per fight, because the WW division in the UFC possesses a stacked house of wrestlers, and that can cause some stylistic problems. They're milking the boxing and money issue for all it's worth, to ensure Nick doesn't suffer a pay decrease when he signs with the UFC. They're trying to make the point that unlike many of the fighters on the SF roster, who have no choice but to sign the deal with Forza, they have other options, and will exercise them if need be.
In the end, I'm pretty sure you'll see Nick sign a deal with ZUFFA, and he'll be fighting in the UFC, barring something going horribly wrong with the financial negotiations. Once Gilbert goes over, he'll be likely to follow suit soon after.