... sigh ...
Maybe morality just doesn't work in an MMO (I've noticed MMOs are generally over-simplified in game mechanics compared to games like KOTOR).
Bioware has taken a couple of slightly different approaches on moralities in their games (Or at least the ones I've played). The two that stand out most to me are Mass Effect and Kotor. In Mass Effect, your morality choices unlock special lines of conversation to help you in the game. This could be from getting extra items, to being able to complete an assignment (Sidequest, in MMO terms). The idea is that if you don't have enough, it's "you're not bad enough to say/do this".
In Kotor, however, your LS/DS points can give you extra great crystals and gear, to being able to obtain extra rewards or credits, or maybe influence to gain exp by talking to a party member. The more you leaned towards an alignment also affected your efficiency in one side of the force (Of course, you have to be a jedi in KoTOR, however in SWTOR, LS/DS is plausible as throughout the Star Wars movies, it's mentioned that every creature is bound together by the force).
In both of those games, morality maximization played a side-reward to enhance your game-playing experience. I do see a difference, as a LS/DS choice in SWTOR is obvious, and a theatrical climatic point in the mission or story, however in KOTOR, LS/DS options are hidden throughout normal conversation. In Mass Effect, small gestures of polite tone or unruly behavior results in small increments of Paragon/Renegade (LS/DS respectively) points. Because of this, morality in SWTOR isn't really worth rewarding, so I do see the opposition's argument of neutral gear.
TL;DR - Morality (in my opinion as a Bioware RPG fan, not super-balanced-MMO fan/ OMG Y U RUIN MY IMMERSION?) should play a part in a side reward in leaning towards one side of the force, and those who do not care to do so shouldn't get slightly better gear.
Again, I understand that in SWTOR, alignment gain is easy to get (say, getting a few LS/DS points). At least in KOTOR and Mass Effect, it was slightly more difficult to get maximum alignment as quickly as possible.
EDIT: And the system was made (as Bioware stated countless times a long time ago to where I'm too lazy to fetch it) to where your choices will have an impact. I know that this means you won't want to go all one side or all another, and you're free to choose that. Bioware Devs also stated that it will determine also the reward gear you get. For all you know, it could be a neutral gear that matches in stats that of the alignment gear.