Nothing is being removed from IRC, only improved. Read the first post more carefully.
Where do you see anything about them trying to kill existing apps? If you read other posts on here, you can see Twitch developers are trying to help existing apps.
JTV was a cancer that had to be removed for Twitch to move forward. Tons of security issues over there, maybe just happening due to its age. There was also blatant piracy going on in their entertainment section (Family Guy, Simpsons, Movies, etc.), which is a liability waiting to happen. Twitch’s infrastructure was also being held back by JTV, as both sites shared the same databases on two completely different sites. JTV was Python+Django and Twitch is RoR.
While there’s missing things from the Twitch API, they may just not be possible due to performance issues. For example, Twitch won’t add the ability to check if a channel has a sub button because it’s too resource intensive for them to pull that at scale.