I really see no other solution than to go with her either before the rain starts or worst case during the rain. As you mention, the current situation is actively reverting her potty training because every day she learns a little bit more that pooping inside is ok.
So if she usually needs to go between 3 and 4 PM and it rains between 3 and 5 PM, then you need to go with her at 2:30 PM. It's easier to change her habit to a time when she doesn't have to go urgently than to have her hold back an hour longer.
Walking usually animates dogs to pee, especially at places where other dogs peed before. Some dogs are also animated to poop by physical activity, others by being in places where other dogs pooped before.