That's right. I got the impression she was driven by mother love and not scientific curiosity. So, as a mother, there is just no way she could have forgiven Hojo, or continued to work with him, meekly and obediently following his orders for two years in the hope that one day he'd let her see her child. Frankly, only a man could imagine that happening.
Let me stop you right there.
Even today, almost 18 months after our son was born, my girlfriend would tell you that I'm the one who displays what she considers most of the maternal instincts, who had The Glow while she was pregnant, and who just has to look at him to feel all-consuming unconditional love. She's said all of this as recently as the past month. And she says that even while she is an amazing mom. My little man is such a lucky little boy to have her for his mommy. I'm so proud of her, and feel more lucky and honored than I can put into words to be on this journey with her.
This is a long-winded way of me saying "I get what you're trying to say." But it's precisely in part because I don't believe the character we're talking about
would that I find her so detestable, revel in talking shit about her at every possible opportunity, and place her only slightly above the franchise's biggest dumbass ever (who fell as far from grace as getting tricked into willingly murdering his schoolmates in "vengeance" for a dead brother he didn't even remember).
Whether as a man, a father, or anything else, I can't rationalize anything that woman did. I can only speak to what, not how.
With all due respect, Tres, you're making the same mistake DoC's writers did.
You're implying the following scenario: Lucrecia gives birth, Hojo (and Gast) whisk the child away without Lucrecia ever getting to see him, she's basically okay with this and the two of them carry on working together as if nothing happened, with Vincent continue to bodyguard them as if nothing happened, except maybe she asks from time to time if she can see the baby - but maybe she doesn't even want to see "her baby", maybe she just wants to see "the experiment" - and then two years later for some reason Vincent decides it's time to object to the situation, and Hojo shoots him, at which point Lucrecia starts getting hysterical about access to her son.
This scenario can only work if Sephiroth, as "her baby", really didn't matter to her at all, but then what could possibly have happened to make Vincent, after two years, object to the situation? It can't have been something that happened to Lucrecia, because she's still in the lab, looking perfectly healthy and with full access to all the equipment, after he has been shot. That's a big chunk of untold plot.
You answered your own question: Perhaps Lucrecia finally started to recognize "Hey, that was a baby. My baby!" and feel like the miserable piece of shit she was. And then, young Vincent -- who had the worst taste in women, like, ever -- was upset about it. "Why did you let this happen!?" he awkwardly demands. He's told to be silent, then shot. Lucrecia actually saves him, but otherwise continues being useless and awful.
Your question about how she could accept any of this applies whether she started to feel like a mother should two seconds, two days, two weeks, two months or two years after Seph was born. She still didn't do everything she could have.
Christ's sake, she had the planet's kill switch locked in a tube, the means to "let it off the leash," so to speak (and restrain it again) -- and she never made an effort to use it? Neither as a bargaining chip, a threat, or a last resort nuclear option?
She just "meekly and obediently," as you described it, muttered "I can't take it anymore" and went to lock herself in a cave. Utterly useless.