It's still open source and you can still compile your own version, but nonetheless the developers deserve a tiny bit of compensation for the work and support they provide.
I'm quite sure that other people have already helped out at the source code. That is the point of being open source.
Anyway, I think that such a basic and central application for MacOSX should always be free and open. And if it is not free or not open anymore, the logical consequence would be to have an alternative project for this kind of application. And it would be a logical consequence to base this new project on Growl.
Thus, a fork.
Growl remains free-as-in-speech and free-as-in-beer if you're willing to compile it yourself. The $2 fee only applies if you obtain the app through the Mac App Store, of which a mere $1.39 goes to the project's developers.
So where is the code of 1.3.1? Even when it will be released once, why not immediately? With 'open development', I also really mean open development, as in other open source projects.
Anyway, as others said, this is still not an option, it still should be free. For example, in my own free and open applications which depends on Growl, I would distribute a free copy of Growl now because I want my users to be able to use it for free. And that goes for most Growl-using applications.
I would not integrate with Growl at this point because I do not believe in nickel-and-diming people and gotchas, but that is exactly what people would find if they boot up my app and discover they need to pay $X for full functionality.
As I said, you can compile your own copy without forking and without paying. But forking with the sole intention of making easier for others to avoid paying is poor form, if permitted by the license.