I doubt Hiruzen would have helped Itachi and Shui take over only to then be like "Well, that settles that!" and just move on.
No, I think if Shisui had taken over as clan leader, immediate changes would have had to follow, changes that were for the betterment of the clan to win over the moderates, thus showing them that the hardliners had it wrong. It could have gone down similar to when Madara lost support when the union of the village was demonstrably beneficial. Both Itachi and Shisui were spying on their clansmen and thus had to know about specific grievances. They wouldn't be able to turn things around instantly, but there really was no reason not to try. The situation definitely wasn't dire enough to warrant the slaughter of the entire clan.