MNTA's methods won't be so easy to copy if MNTA protects them as trade secrets instead of disclosing everything in patent filings.
All told, the situation is not as black and white as you make it sound. Even after an adverse ruling in this case, manufacturing patents for FDA-approved drugs may be enforceable in certain circumstances. Moreover, Congress could change the law with respect to the Bolar exemption.
This story has a long way to go before definitive conclusions can be drawn, IMO.