Faith does not necessarily mean religious faith - the term is also commonly a poetic and secular one similar to the ancient Greek word 'pistos', denoting concept in which you have comforting trust (in, say, a philosophical idea like the redeeming quality of love, or a civic idea) - it may be used in an irreligious context.
But when has pop TV ever risen to the level of making that distinction? (Actually probably only in Picard's nuanced speeches in TNG, or in something like Babylon 5 with it's Carl Sagan/Lord Tennyson-quoting). TV's overt depiction of philosophy has largely regressed since those days. The faith vs. science thing thus sent alarm bells ringing for me. What passes for discussion of metaphysics on TV is usually just scientifically illiterate mysticism and 'woo woo isn't it spooky' self-deception worthy of a 'ghosts-caught-on-camera' show. Quantum mechanics for example, commonly abused in pop culture as 'quantum mysticism', is a theory which actually says nothing any more spiritual than old mechanistic Newtonian physics - it's implications are neutral on value judgements - but is used to justify wild pseudo-religious assumptions, simply because it is complex enough to bamboozle. The first 1.2 seasons of this show felt like that; the spore drive honestly came off as quantum mysticism, but thankfully the show seems to be getting more grounded in reality lately; I thought this might be the influence of Michelle Paradise, but have no idea.
I agree with Longinus completely, that the concept of "science vs. faith" would have likely been an utter disaster. Star Trek may not be above metaphysical speculation, but is a staunchly secular franchise, that finds it's answers inside nature; tender observations about human nature, and the natural world. There is no contest between science and faith - if your faith requires a rejection of objective fact, it is unhealthy. If it helps you with unanswerable nuanced questions like "how can I make peace with an uncertain future", fair enough, I'm all for that kind of belief. Our highest loyalty is to the truth; how can one ever be content with a belief that they know deep down contradicts impartial research on a natural phenomenon, or builds an edifice out of too many shaky assumptions? We all want to know where the universe came from, and where it is going; religious and none religious alike - but we certainly don't need to return to a time when dogma required us to actively misinterpret events or censor our conscious; how could we and also live with ourselves? You can't bury the truth; and who would want to put the wonder of science back in the box now?
On another note, I understand why people were not too entertained by the Red Angel's reveal. It's disappointing that in sci-fi, totally incredible concepts like "it's a 10,000,000 year old survivor from a previous civilization, it's silent cities orbiting a dead star, come out of compassion to prevent the downfall of a younger one" have given way to "it's the character's mom/dad/sibling/self". In an attempt to humanise the genre, modern sci-fi often just wastes the inherent potential of a vast cosmos, full of deep time, and countless eons of possibility. But, at the same time, I still think the show has improved over this season - it could have been handled worse - the last few have felt a lot more rational.