Regardless of how you feel about feathered dinosaurs, the book provided two "outs" they can easily incorporate into the movie:
1) The Jurassic Park dinos aren't 100% authentic natural dinos. A big chunk of their DNA comes from modern-day amphibians and reptiles, which can account for their more reptilian look. (This also works as a general handwave for the story: any unscientific facts about the JP dinos can be attributed to this as well.)
2) Even if that doesn't, the Park isn't committed to creating an authentic reproduction of what actual dinosaurs would have looked like. They're a theme park selling people on the popular perception of "Real(tm)" dinosaurs, and most people picture dinosaurs as giant lizards, not giant roosters. There's a conversation in the novel where Dr. Wu, the geneticist, tells Hammond the dinos they've engineered are really fast-moving, but he could start from scratch and whip up a new batch that fit the slower, lumbering brutes their customers will escape. Hammond rejects this, but mostly because of the expense. In any event, reproducing prehistory accurately was never their mission statement.