No, he was going to assault her but he couldn’t go through with it so then he tried to make her his queen so he can be the king but she refused him and he threw her in a labyrinth for decades until she finally escaped and had to go into hiding for more years.
Long story short he was intending to assault her but couldn’t do it in the end.
You might need to reread chapter 39. Seth never suggested they run away together. Only in the present, he suggested it to her that they should team up against Osiris. But the problem is that *in the past*, before managed to Isis run away, he failed to communicate that intention properly. In the past, according to Seth's own words, he captured Isis and asked her to sleep with him, she tearfully refused, and that's when he threatened her with raping her, so Isis tearfully told him "Neither you nor I will ever get what we desire", and that's how Seth first knew Isis had cursed both herself and him to not obtain what they wanted (he never heard the other part about his family). Though Seth considered raping her, in the end he wasn't able to make himself go through with it, but he at least let her believe that he would, in order to scare her. Then he threw her in the underground prison, and later on, she escaped.
I saw one of the comments say Seth tried to rape Isis and I'm wondering, didn't he say that he told Isis that they could run away together and stuff? but Isis refused and she said "bla bla no family bla bla no love", but he didn't really try to rape Isis? Correct me if I'm wrong but like he never really tried to rape Isis?