She could just be following her husband‘s wishes. As much as she may hate Rhaenyra, not many women would side against their husband in this world.
Another thing too, she suggested making Baela the heir of Driftmark instead Rhae’s kid. Marrying the girls to Rhae’s boys ensures one of them will at least be the Lady of Driftmark. If Rhaenys sided with Vaemond then her granddaughters get nothing.
If Rhaenys agreed with Vaemon he'd likely wed his own trueborn children to her grandchildren, especially since doing so introduces the dragon rider gene in there.
Her grandchildren still get great marriages and it's not the the b*stard sons of the woman who cuckolded her son and then probably had him murdered so she could marry her own sociopath uncle.
Vaemond was right to protest as he was literally watching his house be usurped for the sake of a Targaryen princess.
People like Daemon and Rhaenyra so it's boo Vaemond but he was basically Stannis in the books when his first hand tried to secretly make a match with the Lannisters for Shireen.
It reminds me of what Jon Snow said in the Dragonpit in season 7.
"Words have to mean something, or there are no more answers, and only better and better lies.”
Vaemond saw his ancient lineage being consumed for the sake of Rhaenyra's three little lies and tried to stop it.
The love Daemon gets is proof to me that people really are dumb as rocks.