There has been enough written on this issue, that I don't really need to add anything else.  So here are selected sites with plenty of reading material to help you decide for yourself what the best strategy is to address the problem of pregnant substand abusers.

In response to South Carolina's legislation that made substance abuse during pregnancy a crime punishable by imprisonment, twenty Amicus Curie briefs were filed by various agencies and organizations, including National Association of Alcoholism and Drug Abuse Counselors; American College of Obstetricians and Gynecologists' National Association of Social Workers, Inc.; American Nurses Association; and National Council on Alcoholism and Drug Dependence, Inc.  The briefs all claim that enactment of laws that call for imprisonment of pregnant women who abuse alcohol and other drugs would not be a deterrent to substance abuse, but would be a deterrent to seeking treatment. 
[http://www.drugpolicy.org/library/whitner3.cfm]

The American Medical Association, the American Academy of Pediatrics, and many other group formally oppose criminal prosecutions of mothers of drug-exposed babies.
[http://www.shepherd-express.com/shepherd/21/32/cover_story.html]

"Society is effected by the increased health care costs and educational expenses attributed to the affected fetuses that grow into affected children and adults. Therefore, prevention of substance abuse by pregnant women should be the focus, and not criminalization as an ineffective deterrent."  Pregnancy, Maternal & Fetal Rights, and the Effects of Maternal Drug Abuse on Society: Annotated Bibliography
[http://academic.udayton.edu/health/01status/98duke.htm]

Governmental Responses to Pregnant Women Who Use Alcohol or Other Drugs
[http://www.drugpolicy.org/library/governmental_response_p1.cfm]

The Future of Children, a publication of The David and Lucile Packard Foundation, offers a common sense approach in this article: Interventions with Pregnant Women Who Use Drugs
[http://www.futureofchildren.org/information2827/information_show.htm?doc_id=77253]

Dr. Ann Streissguth at the Fetal Alcohol Drug Institute in Seattle, Washington, has a program for comprehensive treatment of women who abused alcohol during pregnancy, called P-CAP, that has proven successful, and is compassionate as well as effective.
http://depts.washington.edu/fadu/FADU.projects.html#B23P

To understand the problem, one needs to understand addiction and the plight and history of the woman who drinks or uses other drugs during pregnancy.  Here is a collection of articles and links about why women drink during pregnancy and why it is so challenging to find viable solutions.
http://come-over.to/FAS/BirthMothers.htm

This speech by Dr. Sterling Clarren describes his studies of the backgrounds of the birth mothers whose children were seen in his clinic.  This talk helps to clarify why prosecuting substance abuse during pregnancy would be neither effective or ethical.
http://come-over.to/FAS/Whitehorse/WhitehorseArticleSC1.htm