Baiken's chain move used be 12 frames, so it could still get counter hits on lvl 1 moves (since the moves still have some recovery). A perfect buffered counter used to counter hit Sol's 2P iirc, but it was a pain in the ass to do consistently.
Also, keep in mind that you can low profile Sakura's hit-box (unless that's changed too, but I don't think it has). So, moves like Sol's 2D will still go under it. And Sakura's not invulnerable anymore, so Sakura FRC can be a bit harder to utilize in making the move safe. And you can still throw Sakura attempts.
It's generally unsafe to abuse Sakura, and no matter how good your timing is, you will not land perfect buffered counters every time. Even if you could, your opponent won't time things the way you think all the time. People mess up oki timings, and the flow of match makes perfectly timed buffered counters impossible to do all the time, or even most of the time.
People can also delay their attacks slightly (like a just slightly delayed oki) and get a counter hit against Baiken's 2S (Sol, for example, can do this with with a delayed 6P on wakeup, and that leads to lots of damage). Then again, I think Baiken should be able to option select that with FD (since the first two frames of 2S can be cancelled to FD), but she can still be thrown. Of course, she can also add in a jump there, but then she gets vulnerable to lows. Baiken's got ways to abuse Sakura but there are answers to it, which Baiken has answers to, which have their own answers from Baiken's opponent, and blah blah theory fighter. The point is, the move isn't full-proof, and the application of how to beat the move is anything but impractical -- in fact, the answers to Sakura tend to be easier to execute consistently than Sakura itself.
Overall, I don't think Sakura is broken, or even close to it. It's strong, but there are ways to deal with it.
And my own simplified tier-list opinion:
A bit better than everyone else: Zappa, Faust, Dizzy, Millia
Everyone else: Everyone else
A bit worse than everyone else: Robo-Ky, Bridget, Venom