The Usenet joke is not about Sagan’s pronunciation of billion. Rather, it’s a joke unit of measurement called the sagan which is defined as “billions and billions” (however you spell billion). This is probably funny only to technogeeks, so don’t feel bad if you don’t get it.
Whether Sagan actually said “beelyuns and beelyuns” on Cosmos, he claimed he didn’t. It’s been years since I’ve seen it, so I couldn’t say myself one way or the other. He did say “beelyuns” by itself a number of times, though.