Rashi or any mefoiresh on the Chumash is meant as explanation to the pesukim in the Chumash-they do not contradict the Chumash. If they appear to contradict a pesuk in the Chumash you are interpreting the mefoiresh wrong.
Or you are interpreting the chumash wrong, like the tzedokim did?
In our case, the meforshim who hold that Yaakov is physically alive are very clear (you only read Rashi, not any of the others whom I referenced).
You have a question from a posuk, and Ramban there answers. End of story. There is no contradiction between Torah Sebiksav and Shebaal Peh here.
Again, saying that one should always change the pshat of a clear Chazal/meforash to fit the literal meaning of a posuk (especially one which was already discussed and answered by meforshim) will usually lead one to Karaism (as we see from a poster who recently joined this thread).