While lead qualification through workflows is currently not supported, one approach that we saw implemented by a customer that did not result in duplicates is by redeveloping the lead qualification workflow using the msdyncrmWorkflowTools (1.0.54.0): QualifyLead step.
Dynamics-365-Workflow-Tools/Qualify Lead.md at master · demianrasko/Dynamics-365-Workflow-Tools
This was verified to result in no duplicates as the workflow writes the "Create [Qualify Lead]' operation type to the Marketo Log which is like the standard qualify button.
Should there be any further assistance needed in developing the lead conversion workflow, it's recommended to engage with our Professional Services / Consulting team