I am not sure why on earth their doctor would say they needed to use condoms while she is pregnant. In a normal pregnancy, there is no risk to the baby during intimate marital relations. Unless one of them had an STD? If that is the case, the doctor might be worried about transmission to the baby. In that case, they should abstain until after delivery and recovery and find out what other kind of options they have to protect the uninfected spouse from the virus.
If your sister-in-law was raised in a Bible-alone type church, as I was, then you could point to the story of Onan as reference for why not to use condoms. Some people think Onan was killed by God for masturbation, but the story actually is that he refused to (putting this delicately, it’s a family forum!) complete the marital act with his brother’s wife (Levirate law said that when a man died without heir his brother had to impregnate his wife to raise an heir for the dead husband). Thus, Onan was killed for using contraception, what we call “early withdrawal” or something like that. No it’s not a condom, pe se, but it was intended to have the same effect–thwarting conception.
I highly recommend www.ccli.org also or www.omsoul.com for more information. CCLI is mainly info about Natural Family Planning. One More Soul is about why not to use contraception and how to have a welcoming attitude to fertility and babies in the first place. By the way, your sister-in-law (to be?) is nonsensical in her argument against NFP. The point in learning the NFP method is to determine your body’s particular unique patterns. She might be thinking of the old rhythym method, which was a one size fits all theory (which didn’t work for many women).
As for whether it is a sin to use condoms while pregnant, that’s too much of a conundrum for me. Try the “Ask an apologist” forum if you don’t get a good answer here.
Congratulations on becoming an uncle!