I don’t know if Star Trek ever had a really strong coherent overarching morality, but it certainly doesn’t now. The Disco and newer shows are such a mishmash of different people and a different time that they seem often the opposite of what people thought TOS and TNG might have been. DS9-Enterprise were kind of the “in-between” IMO. So there’s at LEAST 3 different sets of sort of framework for what the canon/story/morals even are that it’s kind of hard to discuss as a whole coherently.
Then there’s always the people who take stuff as “cool” that the show didn’t want to portray as “good”. There are plenty of media examples of “cool” bad guys. Look at all the Ducat lovers in DS9, he was pretty explicitly intended and they thought portrayed as a villain, but a complex one. The whole last season turning him into a moustache twirling caricature was to try and “fix” this “misunderstanding” by a troubling portion of the fans.
The whole Prime Directive waffling is well known to fans, and generally there to specifically create conversation about the colonial vs anti-colonial ideals starting in TNG and morphed over time to now. I don’t think the show in a meta sense promotes the prime directive as a good thing - the amount of character struggles and flat out breaking it makes me pretty sure it’s a “no obvious right rule” exemplar.
Disco and on is generally so poorly written that it’s hard to say if they have a message to push inside the show. Most of what we know is from Twitter posts and interviews cause it’s so hard to tell what’s supposed to be the point of the actual show in many cases. With Georgiou I think they’re trying to tell an anti-hero redemption story of some sort. Some idea that anyone can change and deserves a new chance (I think it’s beyond second here). Take out the extremes for the drama and being a show and this is about as obvious as the prime directive as an ideal. It’s not the worst, but I can’t say it’s always valid either IMO.
I think you get from Star Trek what you decide to take from it - it’s entertainment first, not moral education.