Typically, the copper IUD prevents fertilization. Current studies show that the IUD works mainly by creating a hostile environment for the sperm, which prevents fertilization. There is controversy as to whether it sometimes also leads to abortion of a fertilized egg. Rabbis are aware of these factors and widely favor use of the IUD where hormonal contraceptives are not appropriate. Staining on the IUD or the pill is subject to the same laws as other stains. Some do make a woman a niddah and some do not. (See our article ketamim for more details.) When a woman has become a niddah through staining, she waits five days before counting seven.
We recommend that you get back in touch with your rabbi. You could explain to him that your doctor has assured you that the IUD would be the best, most effective contraceptive choice for you. Studies show the IUD to be 98% effective. Although some cases of pregnancy result when the IUD has been expelled, a woman can avoid this by checking prior to relations that it is still there. This is done by seeing if one can feel the strings that protrude into the vagina and can be done as part of mikveh preparation. Since his objection was based on his understanding of the medical efficacy of the IUD, he should weigh your doctor's advice heavily.
Although it sounds as though you have some misgivings about using the IUD, based on the medical and halachic counsel that you received, you should give it a try. Should a problem arise, chas veshalom, please contact us.