You're asking for MTGO v5, not whatever this is. The chance that they're going to completely cannibalize MTGO doesn't seem very high to me. I don't ever expect a Duels-type game to ever have drafting at all.
All their competition has some form of drafting so it would be insane if they didn't in arena. Even the name of the product is the name of Hearthstone's drafting mode. Maybe they could do the simulated drafts like Eternal if they wanted to separate Arena and MTGO.