A major Spider-Man villain being dead from 1987 to 2009 is kind of a huge deal to brush off. And, yeah, the story resolved itself - as a good story should - but as you say, the effects of it were felt for many years afterwards in many follow-up stories. Even the very next issue from a different writer keeps the continuity with Peter admitting he's not back to 100% and is still recovering from the ordeal. DeMatteis has never had a problem revisiting the themes and aftershocks of a story further down the road, and stories like Soul of the Hunter are very much tethered to the events of Kraven's Last Hunt. They explored his PTSD, his guilt over the events, the struggle to recover and find peace with himself, etc. That's the opposite of "everything went back to normal", while still using the medium effectively for self-contained arcs.
Given Peter's misunderstanding and rejection of it, no, I disagree here. It was a transitive moment that ushered in the next step of its journey, because its confusion, anger, and desire for companionship are not just essential to why Venom was interesting from the outset, but also what eventually paved the way for a proper reconciliation and character growth for them all.