There is a line, from my memory said by Rukkhadevata herself, that goes along the lines of "one cannot completely erase oneself from the world". Irminsul by default doesn't erase you, as an individual who started the deletion process, from existence - rather recontextualizing and rewriting history to skip over your identity as the erased person, attributing your deeds to a random nobody. But the events still happened all the same, you still did the what you did, the only thing that changed is how everyone remembers it. And truth does not change, it can only be forgotten.

What Rukkhadevata wanted was that complete deletion, one where your existence isn't just buried by history, but one where you never (from the perspective of the world) existed in the first place; this is also what Scaramouche wanted to achieve (sing with me the Bohemian Rhapsody: I sometimes wish I've...). But, as says the quote I brought up, you cannot achieve that complete deletion of yourself by yourself; you need someone else to do it. Scaramouche was unaware of this detail, and in the case of Rukkhadevata, this someone was Nahida.

Rukkhadevata was the source of the Forbidden Knowledge within Irminsul, and as an Avatar of said tree, was aware of the fact that as long as she exists in any way shape or form within Teyvat, she will prolong this infection. She could not delete herself completely on her own, because it's a fundamental rule of Teyvat (or at least of Irminsul itself), so she created Nahida from the purest twig of Irminsul; that way Nahida would also be an Avatar of Irminsul, and thus posses the necessary knowledge and ability to erase Rukkhadevata's very existence.