According to the documentation of the Word Object Model it is not possible to set fields of sources. However when I experimented with it back in 2007 when the feature was first introduced, I noticed that you could change properties of a source as long as the properties were originally defined. You could use this 'bug' to your advantage to remove the comments with a macro like this:
Sub Test()
Dim s As Source
For Each s In ActiveDocument.Bibliography.Sources
If InStr(s.XML, "<b:Comments>") > 0 Then
s.Field("Comments") = ""
End If
Next
End Sub