The Space Oddesy music was only used for the trailers since it captured the right kind of tension and mystery that Legendary was going for.
Alexander Desplat's score is going to be all original as far as we know. It's likely going to be heavily inspired by the original themes, but I doubt they'll use any themes from the Toho series.
If they do borrow any themes, then they'll be sure to remix them to fit in with the music already present in the film. After all, music and score is just as important as the video that it accompanies. The coolest visuals without the right audio is meaningless and has almost no impact to it at all.
To demonstrate, play the extended footage without any audio and see how "cool" it is compared to the video with the audio on.
If the old Godzilla themes don't fit with Desplat's score, then they won't be used.