It would be great if Ars had used its security and technical staff to tell us if this is a problem or the minor annoyance that the military says it is. The article amounts to little more than a summary of the drone program and a bit of "he said she said" http://archive.pressthink.org/2009/04/12/hesaid_shesaid.html reportage.
Analyse what they know:
1. It's a keylogger
2. They've been aware of it for weeks
3. They admit that they can't seem to beat it
4. These are isolated systems and it's likely that the attack was via USB drives
Based on those facts, is it likely that this is benign? Are there known viruses that fit this pattern? Who's in charge of this project, and what do they say about it? Is it SOP for viruses to be able to completely beat military security for weeks? What are the possible security breaches? Why attack this part of the system?
There's a lot of questions that could and should be asked. Instead, Ars just repeated history and summarized the press release.