They won't do it initially, because football in it's arrogance doesn't seem capable of talking to other sports about they handle it, but in time, I would imagine that they will come to the same realisation as the NFL, and encourage refs to not blow the whistle on marginal calls that will pull back a clear goalscoring opportunity. Let it play out, and if the runner through on goal was offside, it will get pulled back, but if he was onside the goal can stand. Flag goes up, no whistle, if the player misses the offside is given and no-one argues. If the player scores, the offside is given and VAR can overturn if that's wrong.
That's how I'd deal with it, but I'm sure the fantastic brains trust of the footballing authorities will come up with something better.
To me that's the worst thing about VAR. For me one of the great joys of football is the surge of exhilaration when your team score. A quick glance to the linesman is the most any of us do. If the officials are going to let play continue on the grounds that the legality or otherwise of the goal can be decided ex post facto then for me that feeling will be completely neutered.