I agree with both sides on this topic. I think that something along the lines of HaxePunk is the direction to go forward. Over the last few months I have checked it out quite thoroughly and am in the process of "porting" my current project to HaxePunk.
Just the fact that without almost any work you can compile your game not only to flash, but also to desktop (PC, Mac, even Linux!) + mobile + html5. That's so awesome.
And especially since a lot of people are moving away from flash and the whole uprising of greenlight and itch.io and stuff like that, if you want to make a bigger project or even something that you can get something back from flash is not really the way to go.
That said, if FlashPunk had the possibility to publish on desktop I would very much stick with it. The community is so much better!! There is a lot more going on here than in the HaxePunk forums, more people, more open to newcomers and lots of tutorials and code snippets. Haxe isn't all that difficult getting started with but there is nobody to tell you how. The documentation and guides of HaxePunk are pretty horrible, even the site looks kinda crapy (I mean compare it to HaxeFlixel!!! They are a lot further in that regard, and the community seems way more active).
And in the end i just love FlashPunk.
I think that HaxePunk could be just as great if only more people would contribute and try to get a sort of community together. So in the end I woudl say yes to a merge. but I have no idea to what degree and how you could make that possible.
But it would be cool to have the best of both worlds. And it would be really crap if this community declines because people are turning their backs on Flash.