It means it is a choice. Just not the acceptable one.
When Madison says "negative and preventive" rather than "positive purposes", does it mean "positive purposes" is also an acceptable choice?
No, it means that "positive purposes" is a choice, just not the best choice to describe the reasons behind the interstate commerce clause.
This does not mean that the interstate commerce clause cannot be used for the positive purposes -- it can and it is. It just means that "for positive purposes" does not best describe the original reason why the interstate commerce clause came about.