Marvel's high degree of success in the film market was supporting the comic-book market, which isn't exactly in freefall, but isn't as great as it's been in the past.
They probably could've survived as an independent company almost indefinitely, but the Disney acquisition allows them a lot of latitude in areas like film and television. This could mean getting all the Marvel film franchises under one roof, for example.
As was pointed out elsewhere, this also kicks the lungs out of Universal.