I do not think that non-linear levels hurt the game.
In my opinion level design is like flavor - some like specific, other both. While linear levels provide focused experience, NL levels are more like theme parks or/and spaces to realize specific ideas (Lectracity).
Of course NL levels are not as cost efficient, as Ls - and that is for every open world game - most people go to specific place once and then move on: consume the content.
Backtracking can be good if done correctly - it shows different panorama, secrets, approches to combat (like dust2 - site retaking from tunnels and mid/ct spawn is different experience).
But it doesn’t mean that it should be thrown away - I like side quests and activities, exploration and atmosphere. Any Borderlands wouldn’t be the same if it was corridor shooter only.
Of course, if one reduces BL experience to farming only, then anything besides 2 points connected by line is time waster.
Also, if someone is interested, I recommend checking out graph theory and its connection to movement - it might help to describe difference between Athenas and Lectracity at the most basic level. Theory usage can be expanded to sight/shooting.
tl;dr map design is hard.