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Which instance is being affected? your on-premise marketing instance? for these kind of issues only Adobe TechOps can help.
You could liaise with your db administrator to correlate database performance during execution of this particular procedure or setup a monitoring job to check for long running SQL query executions to find out if there is a pattern that can be tracked down to workflows execution which could be running heavy queries. Furthermore you may perform a database health check while at it to check for index fragmentation in the big tables.
Also, what are the settings on the deployment wizard for data purging? are they on default or have these settings been increase which means you may have more data in the metadata tables. what are your database server hardware specs? is it a VM on the cloud or a physical server ?
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