One thing that stands out in this decision is that it makes a plain textual argument that discriminating against someone because they are gay or transgender is discrimination based on biological sex. Given this precedent, it is hard to imagine anyone discriminating against LGBT folks being able to use HHS's rule as a defense.
It would have been nice if SCOTUS explicitly referenced the recent executive order in their ruling. Perhaps the timing of the order (three days ago) was deliberate.
The timing may have been deliberate, but either way as that EO wasn't the exact topic of this ruling, I'm fine with them having left it off. There are several issues this ruling leaves undecided, most critically the issue of sex-segregated locker rooms and bathrooms and the issue of how much protection the RFRA gives employers. But this ruling, I think, will mean that any exceptions are going to require a very strong argument.
I'd be content with a required gender-neutral third option and no god damn bathroom bills. Locker rooms especially need some kind of required more-private area; society has a long way to go before I'd be comfortable using the group shower in either of the locker rooms at my university's gym.