Apparently Massachusetts Transit thinks that it is actually possible to retract information from the public once it leaks.
They've convinced a judge to issue a restraining order to prevent MIT students from presenting at Defcon. But they missed the fact that the presentation is already downloadable from public sources (MIT's student newspaper), is available on the Defcon CD, and then a "copy of the entire presentation was entered as evidence in publicly available court records".
The source code for the nifty toolkit might be harder to obtain. But because is was once public, odds are that someone grabbed a copy.
In any case, the physical security at MBTA was apparently weak enough that many opportunities for mischief were available without going through the trouble of hacking the cards.