They most likely removed it because the third filler story arc has religious references and blood up the hazoo. I don't expect them to put it back on, or YYH for that matter, without severe censoring. (They cut out alot of the good stuff from the Shishio arc when they put it on CN anyway.) That, and Toonami's only on once a week now (unless it got removed entirely, I haven't seen it in awhile.).

Read the manga. The filler arc is nice, but it reveals nothing about Kenshin's past, and the third storyline in the manga has all the stuff you'd want to know And Samurai X seems like a completely different show. (It is an OVA, though, so...) It also has a different ending then the manga's.