It is not necessarily as bad as it may seem. Boeing could have been reporting, and the FAA monitoring.
I suspect that to be the case.
If these batteries were being flagged up by the system as 'below minimum voltage/discharged' and simply being swapped out for new units under warranty, the regulator may have seen the problem largely as an economic one for Boeing.
I agree with you though, that such a failure rate should have set alarm bells ringing at both the FAA and Boeing.
BOEING should have ask themselves:
"What's wrong with the batteries?"
I'm sure they did and I'm sure there were some 'interesting' phone calls between Boeing and Yuasa where Yuasa were telling Boeing's engineers to look at their charging/monitoring systems and installation.