More hints that the Earth Alliance isn’t a shiny happy Federation utopia – they name their exploration ships after conquistadors.

I'm not sure this is an intentional "EA is more sinister than the Federation" plot point, JMS seems to defend it pretty hard in his comments.

I think the problem with the solution in this episode is that as fans of B5 we don't expect technobabble, so we expect to understand any technological solution given. Just pretend JMS accidentally channeled Roddenberry for a moment, and Keffer escaped by remodulating the polarity of the neutron flow in the aft sensor array.