This is probably not a supported way of handling this but we hacked this behavior by shutting off the scheduler search processor for the interactive search head and pooling with another search head that was left as the "job server". This job server would pick up and run scheduled searches while the interactive server could still be used to schedule searches. Not a perfect solution and there are other issues like trying to change scheduled search run times from the interactive search head.
See
.../etc/modules/internal/scheduler/config.xml
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