Lets also not forget that the ending of X3 in film and novel were a bit different from one another. So if Venom takes a big fall or appears dead in the context of the novel, we should still keep an open mind.
Going back to Revenge of the Sith novelization, there's another point the consider - novelist perspective. Along the same lines as merchandising, it's smart to remember that things aren't always as they seem (Lizard among the figure assortment, for example regarding toys). Novelists are allowed to take certain liberties and go places the movie doesn't go, and we may see this very shortly - and it could go many ways.
In short, don't expect to see it just because it plays out in the novel and don't be surprised to see something that the novel doesn't include. The comment about story flow is a great point, but sometimes clever subtleties are the msot magical movie moments. If the novel says the symbiote is dead and is laying in a big motionless blob, don't be shocked if the movie shows that sucker crawling off into a dark corner or down a rain gutter...