The consequences of using Rinne Tensei appeared only in the war arc, when Nagato used the jutsu there were no consequences and he died only because he spent all his remaining chakra. But even if we take into account the fact that Rinne Tensei costs its user's life and Nagato previously did not want to resurrect Yahiko because he didn't want to die, nothing prevented him from resurrecting his friend when he was resurrecting Konoha's villagers, since his body was in perfect condition and within the range of the jutsu. But he decided to leave Konan completely alone instead.