Even if Shao Kahn won the tournament, he wouldn't have been able to merge it anyway because of Sindels protection. Shao Kahn wouldn't be able to walk nor merge the realm despite winning the tournament. And even if he could, the Elder Gods would still step in because that's only when they could intervene, after the events of Mortal Kombat, and after Shao Kahn started the merge of both realms. It's kinda a big 'FU' to Raiden because they didn't explain to him clearly. In a nutshell, if the Gods simply told Raiden 'LET HIM WIN DAMMIT THEN WE CAN INTERVENE', then he'd let him win.