It's not a matter of bringing a spec that brings more utility at the cost of DPS. It's the fact that BM was a quantifiably inferior spec in 3.3, with no unique utility. It's like a frost mage arguing that his reduced DPS was made up for by his bringing replenishment, while the ret pally and shadow priest already in the raid scratch their heads.

A guild that gives carte blanche for it's raiders to play the spec that's "fun" for them, rather than the spec that the raid needs, is simply not going to progress as fast as guilds that are willing to adapt to change as it comes. And it's not just with regards to maximizing DPS, it's also enforcing standards of utility. If you didn't force your ret paladins to spec into Aura Mastery, odds are, you didn't kill HLK25. Ditto with prot warriors who refuse to take safeguard, prot pallies who skipped divine sacrifice. Likewise with Warriors who insisted on raiding as arms, despite having a feral druid in the raid, or warlocks who sacrificed massive raid buffs because they didn't want to go Demo. Guilds that entertained these people's fits of individuality did so by sacrificing the progression of the raid as a collective. It's not to say that they made the wrong choice, it's simply the choice they made.

You couldn't be leading progression on a beastmastery hunter. You could have one or the other. I tell my hunters this: "I didn't recruit a marksmanship hunter, I expect you to be the best hunter possible, regardless of what spec you have to be to do achieve that." I tell the same thing to every other pure DPS we use, they are expected to be proficient in all specs of their class, and to use the spec that the raid needs in that particular situation. Some of them have to change specs between fights, say when going from ODS to Maloriak. That's what it takes to get those kills early on.