É! Realmente, aqui no Brasil, damos preferência ao verbo "tomar", em se tratando de sopa. O brasileiro não come nem bebe sopa: Toma sopa. Em Portugal e demais países de língua portuguesa, não sei...
Native speakers of English would say 'My mother and father....
I agree and it's accepted for to have soup but not to eat soup, which is wrong
You actually drink soup, of course. Parents might tell their children to "drink" their soup.
Drink, or eat. Eat is the normal verb, when it's served in a bowl. (But I'm sure you can also say "went to have soup")
source: Online Oxford Dictionary
Can't foram also mean they were?
Yes. Eles foram meus amigos = they were my friends.
Why are"My mother and my father were having soup" or "My mother and my father were drinking soup" not considered as correct answers?
The hint for foram suggests: "had been going"
The answer (as native German) I tried: "My mother and my father had been going to have soup".
Is this valid English? It was not accepted. What correct tense would that be?
No, it doesn't make sense. "My mother and my father were going to have soup" is correct. But, that has a different meaning than the given translation, "My mother and my father went to eat soup."
My mother and father had been going to have [some] soup when the police appeared at the door.
In some contexts your wording is correct.
What is the difference between tomar and comer/beber?