Here's a quote from that article that I think is good too.
“The good news is that, for children that need formula, soy formula is as safe as cow milk-based formula,” said Strom. “As always, the public should be skeptical of accounts that are based on speculation and case reports, rather than proper science.”
Nolan has very rarely had soy products in his life, but not necessarily because of reports about soy making boys "feminized" etc etc. I don't see the need by the media to demonize soy for all people, especially those who are vegetarian, vegan. etc.
The only possible concern I'd have is that soy is a "top 8" allergen.
To the OP - if your LO had been drinking cows milk okay then got some "indigestion" type symptoms after being sick - it's common to have temporary lactose intolerance after an illness. Try probiotics to recolonize the "good" bacteria in the gut.
We used soy milk with my milk allergic child for a couple years until one day he refused to drink it anymore. We still use other soy products such as soy "yogurt" and "cream cheese". For use in cereal and with cooking, I prefer rice milk because to me the flavor is more "neutral". My cow milk allergic child now drinks only water and diluted juice. He gets needed calcium and fats from other sources.