This is one of those tough cases where software cuts both ways. Some people are smart, informed developers that install a trusted tool to monitor their traffic and have legitimate reasons to want to inspect Apple traffic. They're dismayed. Most people are the opposite and this move protects the most sensitive data from being easily scooped up or muddled in easily installed apps, or at least easily installed apps that…
Either Apple doesn't trust Little Snitch and shouldn't let it interfere with any apps, or Apple does trust Little Snitch and shouldn't block it at all. There's no reason to implement this halfway.