Doesn't that go against what Roddenberry told Matt Jeffries regarding the fact that he doesn't want the ship to be a rocket ship.
Not really; Roddenberry said that he didn't want it to LOOK like a rocket ship or flying saucer (despite the fact that they ended up using the design with the saucer anyway), but he didn't say that it couldn't have
rockets. And the nacelles weren't "rockets," per se, they just operated in the same manner (force is ejected out the back to create forward motion). That's why the nacelles don't glow on the sides, and they have "ends" on them for the warp thrust.
But that's just the TOS tech, which was obviously ret-conned by future shows (if you count them as canon).