a) If you do some research into creationist groups like Answers In Genesis or the Institute of Creation Research, you'll see that they don't argue against "change" (even to the point of speciation). They argue that the type of change we see (like the change in the article) is insufficient to account for all of the different forms of life that we see. You are equating any sort of change as evolution, when their "anti-evolutionism" is focused on the Theory of Evolution, not small adaptions like these.
b). That is sort of my point. You mention interbreeding in the definition of species, but viruses don't interbreed at all. Calling these viruses "new species" is not very helpful. It's very arbitrary.
c) The presence or lack of oxygen is not the food source, citrate is. The wild type e coli already has a gene for a citrate transporter protein needed to bring citrate inside of the cell wall (think of the transporter as a "mouth" that is specific to citrate). The problem is that the promoter region for the gene is "inhibited" by oxygen. Without an accessible promoter region, the gene can't be expressed into a protein. The mutation that led to the cit+ genome resulted in a copy of the existing transporter gene downstream from a copy of an existing (but different) promoter that is not inhibited by oxygen. This allows the transporter gene to be expressed even when oxygen is present.
Once the citrate is inside the cell wall, all e coli already have the ability to metabolize it.
So, the change isn't a new food source, it is a change to the conditions in which the food source can be utilized.
Also makes you wonder how the e coli came to have the citrate transporter gene in the first place, doesn't it?