Exactly my thinking, especially if the position in question was in a sensitive federal project. The contract might even have a restriction on what citizen status the personnel had to have.
I would think that if the applicant had the correct visa to work in the US, they would have stated such in the article.
In my (former) line of work, it wasn't enough just to be a citizen. One had to be eligible to hold at least a Secret clearance.
This article seems to me to be a lot of ado about nothing. Or, more likely, it's a leftist attempt to hit all of the leftist emotional buttons that get them into frothing rage against anything pro-America.