I don't think farming was the way SC expected people to play the game initially, but in the end, it simply adds a new way of playing to the game, people have a choice of playing for trophies or resources. I'm pretty sure most farmers would have stopped playing this game for a long time if farming was being made impossible, so in the end, it does benefit everybody.
It's clear SC is now aware lots of people are farming, and you can see the adaptations they have been constantly doing to loot are a clear proof they are trying to balance this in the game.

