You can use the Laserfiche SDK (via a SDK Script activity) to delete specific versions from the version history of a document.  However, you should be aware that doing so will cause your version history to have "gaps" in its version numbers.  Also, the current version of a document cannot be deleted, so if Workflow created the most recent version, it would still be listed.

You would use a script similar to the following in your SDK Script activity:

protected override void Execute()
{
    if (this.ScriptEntryInfo != null)
    {
        if (this.ScriptEntryInfo is DocumentInfo)
        {
            DocumentInfo doc = (DocumentInfo)this.ScriptEntryInfo;
            if (doc.IsUnderVersionControl)
            {
                VersionHistory history = doc.GetVersionHistory();

                for (int i = 0; i < history.Count; ++i)
                {
                    DocumentVersion version = history[i];

                    // replace "Workflow" with your Workflow User
                    if (version.Creator == "Workflow")
                    {
                        // write an appropriate note for why this version is being deleted
                        version.Delete("This version was deleted because it was created as part of a workflow.");
                    }
                }
            }
            else
            {
                this.WorkflowApi.TrackWarning("The document '{0}' is not version controlled.", doc.Name);
            }
        }
        else
        {
            this.WorkflowApi.TrackWarning("The entry '{0}' is not a document.", this.ScriptEntryInfo.Name);
        }
    }
    else
    {
        this.WorkflowApi.TrackWarning("No entry was specified.");
    }
}

One other thing to note is that you would still need to determine when you wanted the workflow to run.