Assuming Spidey appears in Civil War as Spidey we may luck out in this regard. So far the characters Marvel did origin stories for had never been done in movies but they did skip an origin story for Hulk. And knowing there's been two movies covering his origins in the last 15 years I imagine we might get some small flashbacks, but they'll probably be rather brisk and to the point rather than dwelling on him and how he became Spidey.
At least I really hope that's the case.