Is it not incumbent upon the audience to determine if it's good or bad, not being told so by the text? I would like to think that the Trek audience is intelligent enough to figure that out.
I think you are (purposefully?) missing the point. I don't need the program to tell me whether the element is good or bad. Yes, that should be evident from the show, I have my own morality to tell me so independently, and I don't need Trek to spell it out with some overwrought metaphor - like half-black and half-white faces.
But what I need is for Trek to, in-universe, present the element as bad. It goes back to the whole Trek-ian ideal that humanity can improve, that we can be better and do better (not that we always do or that we are always perfect). In Trek, Starfleet and the Federation are idealized versions of what we could be in the future. They don't have to always be right or always achieve that better nature, but to be true to Trek, they need to always be striving for that improved nature, improved being.
Embracing a concept like Section 31, as Discovery has done repeatedly, and presenting it as something good and positive is antithetical to Trek. Discovery has in generally presented Section 31 as something generally good - they have cool tech and cool starships, they have cool AI programs that guide Starfleet strategic thinking, they do the dirty work that the uptight Starfleeters are unwilling to compromise to do, we need them out there, etc. - and that any bad element is only due to the occasional "bad apple" like Control going rogue. This is the exact opposite of what Trek should be presenting. The main characters should not like or trust S31; Starfleet in general should not like S31; a few Badmirals can employ or support it (like Adm. Ross did) but our heroes should oppose them (like Bashir did).
This is what DS9 did right in their original presentation of S31: S31 basically embodies "the ends justify the means"; where the rest of Starfleet, the Federation, and Trek itself says "no, the ends don't justify the means." By embracing S31 as a key element of a show, and not treating it as the anti-Trek concept that that is, is a disservice to Trek.