Upon reflection , I think this article (and others like it) are starting from the wrong place and end up confusing the issue more than illuminating it.
I think the right place to start is that Google wants to offer a premium, ad-free YouTube service. Given that, what happens to videos that are ad-supported today:
1. They participate and are ad-supported for free users and subscription-supported for premium users. Cool. Everyone's happy.
2. They don't participate and...
(a) Premium users see ads anyway. They're pissed.
(b) Premium users don't see those videos at all, but free users see them with ads. Might dodge the issue for a while, but when they find out they'd be even more pissed.
(c) You can't offer ad-supported videos to free users unless you also offer ad-free videos to subscription users. Labels that like the ad-supported terms and don't like the subscription terms are pissed.
Alternative (c) seems to be what Google has picked. Which seems logical if they're launching a new service they want new users to like.
Corollary: Indie labels should still be allowed to post whatever non-monetized videos they want (subject to other YouTube policies like the terrible ContentId, of course). If that isn't true, then we can talk about being "kicked off YouTube". Otherwise, they're choosing to leave because they don't like how the monetization option is changing. That's clearly their privilege, but, in the exact same way, it's Google's privilege to change the monetization they're willing to offer (whether that's as small as tweaking the payout formula or something larger like adding a subscription tier).
P.S. I found some of the Ars Technica comments (not the article) particularly helpful in terms of explaining how this must fit together: http://arstechnica.com/business/2014/06/artists-who-dont-sig...