Do your best to convince your ex to let them have the medical. Explain that having the medical does not mean that the children will be immigrating to Canada, as you can specify that they are non-accompanying and in any case your ex would need to give permission for them to immigrate. However, doing the medical means that the possibility for them to immigrate later is left open. If your ex dies, for example, if the children do not have the medical now, you will not be able to sponsor them later. In addition, the children may want to immigrate when they are older, perhaps for education, and getting the medical leaves this possibility open.
Try to get other family members or friends to talk to your ex about this if she won't listen to you. It really is in the children's best interest to get the medicals done.
If this fails, you will have to sign an affidavit stating that your ex will not allow the medicals to be done, and that you understand that this means you will never be able to sponsor the children.
CIC will probably ask several times for you to get the medicals done, so not doing them delays the processing time of your application. However, it is possible to waive your rights to sponsor your children.