Alicent and Helaena's Fates Already Sealed; Needless to Say, It Won't End Well
You probably already expect most of House of the Dragon's characters to meet tragic fates, even if you haven't read Fire & Blood, the book which serves as the series' main literary source.
Now, the series' scriptwriters so far took some limited liberties with the book, to spare a character or two, but generally it serves as a decent guide to what is awaiting the characters.
And of course Alicent Hightower and her daughter Helaena won't receive happy endings in story.
After death of Prince Lucerys in Season 1's finale, Daemon Targaryen decides to take revenge by arranging the crime known as "Blood and Cheese," which sees the two eponymous assassins murder Prince Jaehaerys Targaryen, the six-year-old son of Helaena and Aegon.
Helaena was forced to not only watch the murder, but to choose which of her children died; it left her utterly broken and described as "mad" in the book.
Not that she is a picture of mental health to start with in the series. Consumed with grief, she eventually falls to her death from the window in Maegor's Holdfast. (Of course, the series can also play with the fact that falling from a window is an excellent cover for an assassination.)
Helaena's death in turn impacts Alicent heavily, as Helaena remained the closest to her out of her three children (though Aegon II and Aemond also perished during the war). While Alicent survives the Dance of Dragons, unlike Rhaenyra and nearly all of the Blacks' leaders, she has to watch Rhaenyra's son crowned as King Aegon III, and dies of illness fairly soon.
While Helaena was clearly one of the few genuine innocents in the whole affair, it is much harder to say whether Alicent deserved her fate.
The answer largely depends on whether you consider the Dance of Dragons to be an inevitability, pre-determined by King Viserys well-meant and poorly thought-out decisions, which piled one political situation likely to cause a succession crisis on another, from the designated heir living in near-exile away from the capital, to that heir being designated in spite of the custom which brought Viserys himself to the throne; or whether you believe that the civil war could have been averted had the parties demonstrated less belligerence.
Not even the showrunners give a definite answer to this question, as they make Alicent and Rhaenyra act as if the war was avoidable, but then show the events getting out of anyone's control and sliding inevitably towards violence, as accidents and miscalculations provide the final sparks for the conflagration.
Anyway, if you believe in the former, then Alicent had no choice but to protect herself and her family, and if you believe in the latter, she was one of the war's chief architects, and created her own misery.