I have simple answer. This is game, game have goal and only actions what brought players closer to goal should be rewarded by xp, no matter what way the chosen to accomplish the goal.
The simplest solution and the best one for balance is to set some checkpoints like: coming to fort joy, finding way in magister's headquarters, getting out of it. etc.
Side quests and killing should only give items and money as reward, because they don't directly help in progress main quest. They will be pure optional choices.
If you want level up you need to actually progress, no backtracking or randomly kill everyone.
That solution doesn't force anything, and is nice gift for people who only want to do main quest only. People who like doing combat, quests and stealing will have extra items, skills and gold.
/// Soft version of that solution would just lesser xp reward for quests and having something like bestiary from Pillars of Eternity.
