The Marvel Cinematic Universe has probably already gone through Secret Wars, it was just restored. Even if it was pre-secret wars, that would just set up a reboot. I say that lightly, as it wouldn't really be a reboot.
I think that the MCU is going to run through phases 4, 5 and 6 leading up to an adaptation of the Secret Wars storyline but they didn't reboot their franchises after that story in the comics and the comics' universe has had the same continuity since 1961 when the Fantastic Four were created and even if they did reboot in the comics, the MCU never follows the comics exactly. I think that the characters who were created from the past will all be gone but they will have new characters to lead the audience into the "next generation" of the MCU as well as creating new fans who will grow with those characters