To my knowledge, Blizzard has not made any attempt to clarify that either version of this story (the 2016 movie, or the original Warcraft I RTS game) should be held as canon over the other.
There have been relatively few times where they have directly commented on canon matters. The majority that I can find relate to differences in characters as portrayed in various tie-in novels and directly in the games, and the general impression is that nothing should be taken as writ in stone. There have been several times where Warcraft history has been rewritten to accommodate the stories they want to tell, simply because the new material is cooler, or just plain newer, or other various reasons. The Draenei example is probably the most famous for stirring controversy, although for sheer amount of rewritten history I understand the newly released Chronicle can't be beat. Bottom line, game canon is a Doctor Who type of "everything is canon-ish" and should align to whatever makes more sense, with newer material having some preference.
The movie is an attempt to retell one of the older Warcraft stories, and doesn't make an attempt to tie to the current game events other than basing off them, so there's no indication of history revision here, other than slightly different plot details. This would be consistent with most video adaptations of SFF media; its a choice to do what works on film (for better or worse), rather than being mandated into lockstep by the original work.
So I would suggest that, between the lack of statement and the flexible canon the Warcraft universe uses, the movie exists in it's own canon, rather than needing to somehow fit into the already zig-zagged lore of the game.
