i think it is just another one of those things that some will tell you it is good for you and others will tell you it is bad. i know several people who do pilates and they all enjoy it too. i think that if you are exercising in a safe environment and in a safe way and you are enjoying it, there shoudn't be any forseeable harm.
however, there are criticisms and as you have back problems you might want to check things out with a professional. there are some thoughts here, in the limitations and criticisms section. but if you read the section above some medical practitioners approve. your individual circumstances need to be considered regardless.
http://en.wikipedia.org/wiki/Pilates