Her only counter play is to focus and kill her, and in a team fight focusing and killing the support means your whole team takes free damage. It wouldn't be a problem if she was actually squishy but no she builds tank and still heals each of her team mates for like 1000 hp.
Raka's heals scale with AP; meaning that if you go full tank, while yes, you'll have heals out the ass, they'll only be doing maybe 100-150HP per heal. And when the cooldown is about 2-3 seconds I believe, that is both not a lot of health and not a lot of time to heal teammates during a teamfight.
Meaning you have two ways of building your Raka; the first being tank, support where you can peel, heal over time, and take damage for your team, or the second being an AP, support where you can not only deal damage, but your heals are massive influence during a teamfight as well as you yourself become a major asset to the team.
Regardless of these how you build her though, Raka always has set backs. For starters, she isn't very mobile. Unless there is a half dead teammate she can use as an anchor to escape, the second best option is to try to kite with your Q. And that isn't exactly the best of slows. So if Raka is tanky, save her for later; her defense doesn't scale the best so killing her won't be like chasing Ali. And if Raka is more AP, it's like you said, she becomes a major target.
As a Raka player, the most efficient way to deal with Raka is taking her our third, after the ADC and mid-laner. Tanks and bruisers are meant to be a pain in the ass, so they need to get your undivided attention to finally kill. And it isn't the easiest to take down Darius when Raka's got his back. So by killing the main two damage deals, Raka's CC and heals over take any damage you may be getting from the tanks or bruisers in my opinion.
Most of dealing and countering Raka is knowing what she will do and how she is going to play. Paying attention to the support isn't always a bad things because, let's all be honest here, more often than not, supports are kind of who carry ass in a teamfight. Point though, Raka's Q is the only ability of hers now that hits minions and monsters. Getting caught in a minion wave and taking a Raka Q to the face will lead to major winion block. The Q, E combo isn't the easiest to land, but Raka is liable to go for the root after slowing you with her Q, so be sure to always watch out for that. Raka's heal uses both health and mana to cast, meaning if you can either bully her out of health or bait her into continual bad poke or engages, then going in once either are down is your best choice.
And most importantly, SORAKA CAN INDEED BE SHUT DOWN AND KEPT DOWN.
While I will agree, no matter how far behind, a good Raka player will always be an asset to their team; however, Raka is very reliant on her items late game.
She is the strongest during early and mid game; early game her self-heals on her Q are unbelievable sustain however drop off mammoth as the game goes on.
Even when going more tanky, Raka is dealing a pretty good base damage as well as damage over time during mid game. At this point, she has likely maxed her Q and has W leveled a good deal, meaning her main damage dealer is dealing the most base damage it can as well as likely is on a very short cooldown now; on top of that her heals are strong enough to get a teammate out of a bad engage.
So to keep Raka down, dodge the Q's, bully her out of lane as much as possible, and if anything, focus her over the ADC at times even.
Raka is an engage support, meaning she is more than likely the one with the real balls in the bot lane. Once the ADC is left without a hand carrying them across the lane, you can run them down with your train. 
It's the boards, just ignore opinions, ignore how she plays and how stupid she is, and just say she has 55% winrate.
That's basically the only thing the boards care about.
