In my opinion Bawolff is correct. There are two competing forces at work here:
1) There are substantial benefits to operating Wikinews (not WikiNews.com, btw. That site is controlled by an anti-WMF fanatic:P) under the banner of the WMF, not the least of which is the partial protection our explicit association Wikipedia occasionally lends us (IE, against government censors). Having an implied association ("Oh sure, we're friendly with the WMF. Look, we even use Commons!") just wouldn't be the same when combating problems that are common to both Wikipedia and Wikinews. To be Henry (Frank is in my bad books right now) Wikinews isn't big enough to fight these problems on its own.
2) As Jimbo pointed out, Wikinews is having trouble thriving in the current 'pedia dominated climate of the WMF. The WMF (rightly) directs most of its resources at its biggest projects, most of which are incarnations of Wikipedia. Everything from the software development to the hardware selected for the servers is controlled by the needs of Wikipedia. And you know what? That's not wrong. Wikipedia is big, and it needs a lot of time and effort put into it in order to for it to be maintained and grown. But Wikinews needs some lovin' too if we're ever going to achieve anything. So does Wiktionary, and every other project as well.
These two competing forces aren't going to go away. The only solution that I can think of that makes sense is something like what Bawolff suggested: keep Wikinews as part of the WMF, but spin it off into a partially autonomous organization that focuses entirely on Wikinews community & software development, with its own mini-leadership council that reports to the WMF board of directors.
Whatever happens Wikinews should be kept non-profit.