They did say that Java MC isn't going anywhere.
Their stated intent is to make add-ons/plugins as powerful as they can, but there is a limitation in that they want them to be able to work in environments like iOS. Add-ons sre no problem: they're just json data files. They think they'll be able use use C# plugins on iOS, but I'm quite interested to see how they pull that one off.
Regardless, there are 30-40 million players of MCPE who have no modding at all today. This new system is going to be a big step up. even if it is entirely different from the way Java MC is extended.
Embrace, extend, extinguish is how it always plays out.
I personally don't think that Mojang would do that unless forced to, especially given what would happen to the community. Most likely established modders would continue to use JMC as their base, pushing new modders towards doing so, and thus it would continue to overshadow other versions, as the mods really do make the game.