[Ol' Dan Tucker]

Compromised POS systems were all Windows systems.

The compromise was at the server level. The hackers installed a compromised server on the network and read the data from the POS terminals in real-time.

IOW, they had insider help or used social engineering to gain admin-level network access.

So, in this case, at least, using Linux would have made no difference at all.

[uncommonsense]

It does look like an inside job:

"But according to sources, the attackers broke in to Target after compromising a company Web server. Somehow, the attackers were able to upload the malicious POS software to store point-of-sale machines, and then set up a control server within Target’s internal network that served as a central repository for data hoovered by all of the infected point-of-sale devices.

“The bad guys were logging in remotely to that [control server], and apparently had persistent access to it,” a source close to the investigation told KrebsOnSecurity. “They basically had to keep going in and manually collecting the dumps"