Actually, "ai" is kunyomi. The onyomi of that character is "go".
Do you know that it is kunyomi or do you assume so just because "go' is also onyomi? It's not a binary thing. There are often more than one Chinese pronunciation for the same character, and thus more than one possible onyomi reading.
合 "Ai" is cognate to Chinese 合 "hé" with the same basic tropes of meanings in both Japanese and Chinese. Both readings are onyomi, from my perspective. The other onyomi you note is 合 "go," cognate to Chinese 合"gě" which is another pronunciation for the same character 合 -- meaning a certain measure of grain or other produce.
While O Sensei valued farming, I don't see a direct or even connotative connection.