Only certain vaccines are prohibited, i.e., those based on aborted fetal tissue. There are vaccines that are perfectly good moral alternatives; FReepmail me if you are interested in a list.
For a list of ethical vaccines, go to the Children of God for Life website and click on “Vaccines using aborted fetal cell lines,” near the top (PDF file).
Think Church allows use of therapies derived from aborted fetal tissue, but forbids the abortion to obtain it.
Like can receive kidney transplant from murder victim while condemning murder.