I absolutely love HomeBrew, it is modeled a lot after MacPorts/FreeBSD ports tree and provides a way to compile packages from source (some are even hosted as bottles... no compiling required). It is an excellent tool to download and install libraries and do development with. Will Apple keep all those tools around? Only time will tell, but so far it is looking good and I don't think it is in their best interest to move away from it.
Keynote was and is a great presentation application. But PowerPoint 2008 surpassed it, PowerPoint 2011 even more. The only major feature missing from Powerpoint is magic move. Other than that, PowerPoint has better table and chart tools, better graphics, and at the very least adjusts font sizes automatically when necessary.
In order to keep such things being developed, Apple will need to provide an adequate development environment.
Thus, Apple has an incentive to keep both worlds alive.
The only thing to worry about is that, because they only have the incentive to keep their development ecosystem merely adequate, we won't see much improvement in developer tools – just slow, linear change. Fortunately Xcode has competition from Visual Studio to keep it going, but whether they will continue offering a competitive BSD development environment is a legitimate question. Most Linux distributions already provide a better experience in this respect, having package managers and user communities and such.
Ultimately, I find the attitude you present here to be a bit overreactive. Lion and Mountain Lion introduce a number of iOS-like features and integration, but as far as I know, the developer tools were not crippled in any way, only improved, a bit.