I imagine it's because it would've cost them to get it; From a business view it doesn't really make sense to have two of the same episode available to stream, even if the OP/ED are different and the omake is different, they'd have still probably been made to pay the same amount as if it were a brand new episode.
If the episode had been changed in a more significant way such as being re-animated in 16:9 or something then I imagine that would have warranted them picking up the new version but as it stands I doubt the little bit of omake is worth it.
Whilst I agree, as a fan of Gintama I would've liked to see this version, I really can't see any valid reason for Crunchyroll needing to get it. They never picked up the first Yorinuki season and I imagine if this were a purely re-run season again they wouldn't have bothered. At least we're getting new episodes!