Madara learned about Rin and Obito's love for her from Obito's stories. Madara himself had agents in Kirigakure he had under the control of his Forbidden Individual Curse Tags. He orchestrated a staged mission where Kiri ANBU and Jonin would kidnap Rin during a mission she was on and seal the Three-Tails inside of her, this particular mission was set up to be one that Minato wasn't on, so he wouldn't interfere. The seal would then be triggered upon Rin's return to the village to release the beast and kill Rin, allowing Isobu to rampage through out the village. To Kiri, this was an official mission, but to Madara, this mission was to set up Rin's death so Obito could witness it. He had the White Zetsu inform Obito of the incident, which then caused Obito to leave and arrive "just in time" t