Currently, the powershell commands for exporting and importing a search don't have support for the report and alert tabs. The only way to disable an alert currently is through the UI.
That said, we are currently working on the 7.4 release branch features, and there is already a story in place to accomplish what you're looking for:
Enhancement Request: 377974: [PowerShell] As a CA admin, I would like the Get-CASearchDefinition command to export the email addresses configured on the alert and report tabs of a search
This would allow you to export the XML for a search, which includes the alert settings, to an XML file, which you could alter to disable the SMTP alerting for, then re-import the XML into a search via powershell then delete the original.
This feature is slated for release in 7.4 with no ETA at this time.
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