No their application will not be refused just because the medical exam has not been completed. The embassy will send a letter requesting the medical exam results - if they have not already notified the embassy of her pregnancy they will need to reply with a letter from her doctor confirming the pregnancy, and that she has to wait to receive the xray. She can have the xray as soon as her doctor says it's safe to do so. Sometimes that can be during the final trimester of pregnancy, but if she has a high-risk pregnancy or any complications her doctor will certainly not allow it until after the baby is born. The embassy processing her PR application will put the ap on hold, knowing that she needs to wait for the xrays, and then will resume processing when they receive them.
No, there is no minimum income requirement for sponsoring a spouse - but he will have to prove his intent to resettle in Canada before they'll issue her a permanent resident visa. Because he is a Canadian citizen the new baby will be one also, so s/he will not have to be sponsored. They will have to
apply for a citizenship certificate for the child so that they can get him/her a passport. They should do this immediately after the birth, and find out what is required for the baby to enter Canada because his wife's Confirmation of Permanent Residence will have an expiration date - she will need to enter Canada and "land" before the expiration date or the COPR becomes invalid and they'd have to start all over again. The timing could get very close - although, normally, a COPR is valid for as long as the medical results are valid (usually a year) and since she won't complete the medical until late in her pregnancy at the earliest, she should be okay as far as the COPR expiration and that should give them time to get what they need for the baby.
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