jiraya only had to place a piece of paper on narutos head when he went into a 4 tailed cloak state. jiraya didnt have to try and harm naruto. he just had to dodge his attacks and place the tag.
One thing i need to add is jiraiya’s sage mode is sage art amphibian technique which is much stronger than normal sage mode as he is fused with two other sages which gives him constant nature energy and there is genjutsu called toad song which doesn’t require time like demonic illusion so jiraiya is highly capable of defeating pain
Jiraiya was stronger than Kage level. They are S-Class which as a class but most who fit in this class are above Kage level seen during the whole series.