Not everything has to do with an agenda. In the mentioned case, it’s basically preaching to the choir. People who are already pro-choice are going to cheer for this plot twist; people who can engage in sensible ethical reasoning are going to hate it.
In painting with such a broad brush, you completely miss everything good about such a series.
Why? For many people that is the reality. I grew up in a conservative Catholic nuclear family home where literally every time I took my mom’s advice it ended badly. If someone made a movie of my life during my teenage years, your quote would have been a central theme.
You entirely mischaracterize this. (a) That’s a personal taste and preference thing. I happen to like it because it gives it an authentic feel without assaulting the ears with the actual word f****. (b) Not at all. Alchoholism is a character flaw. Now, most of the other characters don’t do / say anything because the character in question is their senior officer. This is typical and realistic in a military environment. But there are several points throughout the series where certain characters are called out on their character flaws (including alchoholism). This is usually done by a wise male role model (are you listening, ed?). (c) I am not sure what you refer to here.
Well then you must never have any heroes who are soldiers / other military / law enforcement, because a body count is inevitable in the nature of the job. My young daughters can watch sunshine and rainbows all day, but as an adult I want entertainment that makes me think about hypothetical ethical issues.
I don’t know why you would be a fan of Star Trek, given that Gene Roddenberry dreamed of a world where humanity had outgrown religion, which is very clear at various points even in the original series. Surely you see Star Trek as beholden to the atheist, anti-religion agenda; it would only be consistent with the way you see literally everything else in your world that you have chosen to comment on.
Now, I know why I am a fan of Star Trek, and it is because of the reasons you mentioned, as well as the extremely progressive values for the 1960’s. (A black WOMAN, a Japanese man, and a Russian man (in the middle of the Cold War!) and an alien - ON THE BRIDGE!!! And TV’s first interracial kiss!!!)
The first couple seasons, yes. The actors were all getting their sea legs. Try 4th season on. Particularly 6th and 7th season. Although some of those involve ethical and philosophical complexity, so on second thought you may not like it.
On the contrary, darkness can be very educational. You can watch your heroes wrestle with ethical issues and suffer the consequences of bad choices. A good hero isn’t just one who is mostly perfect; a good hero is also one who has the right underlying principle but sometimes struggles with the application. In watching our hero struggle, it reminds us of our struggles when we mess up. And in watching our heroes suffer the consequences and learn their lessons, we are encouraged to make good choices, even if it seems late in the game for us in our lives.

We actually agree on something! Run for your lives!