Until India became independent, the question wasn't so much whether the diet was balanced than it was whether there was enough food to not starve. There have been a few famine threats since, but thankfully nothing like the 1943 Bengal famine, which resulted in an estimated 2.1-3 million deaths from starvation or malnutrition.
As to the evolution of the diet itself, it seems to have changed somewhat since independence, in that consumption of produce, eggs, and diary have increased. There was a study published a few years ago by the Food and Agriculture Organisation of the United Nations (FAOSTAT) to flesh this out. It analyzed the consumption patterns of countries across the world between 1961 and 2011. (The data apparently resides here, but I can't seem to get the page to finish loading.)
This article on results for India give a summary of the findings:
In 1961 the average Indian had a daily calorie intake of 2,010. Their daily diet consisted of 43% grains (378g), 23% produce (199g), 12% dairy & eggs (108g), 12% sugar and fat (108g), 2% meat (17g) and 8% as other (68g).
In 2011 the average Indian had a daily calories intake of 2,458. Their daily diet consisted of 34% produce (450g), 32% grains (416g), 18% eggs and dairy (235g), 10% sugar and fat (129g), 2% meat (29g) and 4% as other (58g).
National Geographic put those numbers in helpful charts.
This is the gram per day breakdown in 1961 and 2011:
This is the calorie per day breakdown in 1961 and 2011:
The charts unfortunately don't break things down in enough detail to determine whether the assertions in the article you cite are correct or not. Still, they do hint at the notion that India as a country could be eating more, and more diversely. Or put another way, that the local staple foods are still the basis of what people eat day in day out. This leaves plenty of room to increase gram and calorie intake from the nutrients that the article you cite mentions are lacking. Thus, I would hazard the suggestion that this is all due to, to quote your own words, "a significant chunk of the population sustained on bare minimum means for their sustenance" - while leaving the question of who one should attribute that state of affairs to open.