I'm not sure there's an answer for this, but I would suspect that it's because science stands for "objective truth" --- I know that this is not as true as it once was in the days of Newton, but science is capable of creating testable laws, laws that cannot be manipulated by the state. Who contols the present controls the past ... but control of the present doesn't give anyone control of scientific realities. It may be inconvenient for the state to believe that force = mass x acceleration (f=ma), but it's not something that they can change simply because they contol the present --- not, at least, if there's real science around.
The admission that there are absolute truths might give people the idea that there are other "absolute" truths, and that not eerything they are told is true is. This is not in the best interests of the Party's state ... so no science, no absolute truths, just malleability.
Hope this helps.
The purpose of newspeak was to make alternative thinking impossible. To reach this end, certain words had to become obsolete. Science, a branch of knowledge, would encourage people to begin thinking outside the box. That in itself is alternative thinking and not allowed.