The finding is controversial because it has been commonly known that arsenic esters (R-AsO3) are rapidly hydrolyzed in water. For example, the main cause of arsenic poisoning is its replacement of phosphorus in adenosine triphosphate (ATP), followed by the quick decomposition of the arsenated compound, preventing cells from performing metabolism. The NASA paper claims that the bacteria have somehow found a way to create stable arsenic compounds despite the fact that cells are highly aqueous environments. I don't believe anybody is disputing that the bacteria can grow in the presence of arsenic. Rather, the controversial claim is that arsenic is replacing phosphorus. For example, an alternative explanation would be that the bacteria possess very effective mechanisms to pump arsenic out of the cell, similar to how halophiles are capable of removing large quantities of salt ions.
On another note, I don't think it's fair to be attacking NASA about this, though their decision to hold a press conference appears politically motivated (i.e. a grab for money/attention). Their space program is consistently underfunded, and they've been deploying robotic missions as much as usual.
As for whether the paper's claims regarding the incorporation of arsenic into molecules stands up, that will have to ultimately be confirmed by independent experiments. It's not like the bacteria are some kind of state secret, so it's premature to call anything "under fire" at the moment.
Disclaimer: I don't know anything about biochemistry, I'm just another IT guy.