It's about the nature of the game and intention of the developer. Thief wasn't moddable, and still has a big cult following, two sequels and a fourth game in the works. All the while the integrity of their universe stays intact. People know and like that game for what it is. Garrett sneaking around being a thief, the story of the Hammerites and Mechanists, etc. I'm among these. Sometimes modding helps a game and sometimes it hurts it.
One cannot argue that modding in Unreal Engine hasn't helped a lot of people, but has it honestly helped the series itself that much?
It's true that some series are probably left best with out the ability to mod. SP based games like Thief and such need to keep the story intact. But for MP games, I think it's more important.
I think modding has helped the UT series. If not, I don't think Epic would have had the MSUC. Imagine playing UT 3 with just stock maps. Granted, I play this game primarily against the bots, but for me, it's makes a big difference.
Add to the discussion that the ability to mod games also helps the industry as it allows people a way to learn before they get hired and allows them to get hired quicker as they can learn faster and show off their talents.