It is possible to give players freedom while also delivering a great story, just look at Fallout New Vegas. However most open world games fail horribly at this; most of the sidequests in, for example, Watch Dogs or GTA5 are just not that interesting from a story perspective. If a game is going to prioritise one over the other, I prefer they favour story.
That said, story focused games need to be very careful in how they handle antagonist interactions with the PC. In DA2, it infuriated me that we couldn't take out Petrice in Act 1; she sets you up to be killed, you can even threaten to kill her, and then...the game forces you to let her go. Wth? If you want to preserve a character for a future plot point, don't have them interact directly with the PC until that future point. The Petrice thing could easily be solved just by having Petrice not be there when you went back to end the quest; just have a generic templar you can eliminate or let go instead.