You can get Crucible Commendations by ranking up faction reputation to rank 3 and each rank beyond and you're right that you could technically do that by solely doing Vanguard bounties, weeklies, strikes and patrols with the factions class item.
However, the only CURRENCY the faction vendors take is Crucible Marks, which can only be earned by playing matches in the Crucible (2 for loss, 3 for win). Given that, even if you suck playing Crucible and consistently finish with <0.5 K/D, it doesn't take too terribly long to earn those marks or even the bounties for that matter.
I get the knocks on Crucible, but I actually think the latest update notably improved the situation there. That said there are things like overall map design that can't really be tweaked with a patch.