Sorry to say your kinda stuck with you current run and will have to just go with the flow or start a new run. Kate and Isabelle are mutually exclusive routes, though the Season 2 Kate & Isabelle main quest lines do seem to be setting up the possibility to make peace with the girl you went against. Also at the present time no matter what you do Lindsey is going to fall. The only thing you can change about the scenario is whether you stand by and watch or try to save her.