As, yeah, stupid applications is hard to guard against, but stupid applications might/will have their own share of code execution bugs, which you also have to control. Everything sucks.
As for the environment, that's the same for any UNIX, though. .bashrc is run only if you start bash. Getting an ubuntu dist. to set up your environment variables in GUI applications certainly won't be fixed with a .bashrc. It might inherit /etc/profile, if you're lucky.
For OS X, launchd handles the environment by simply being the one responsible for starting the applications that you inherit your environment from (such as Finder, Dock and Spotlight), and .bashrc is just a file that bash executes itself that might set additional environment variables. This is not unlike a Linux setup, where you only inherit environment variables written in .bashrc if you started the application from bash.
(OS X does have a path management system for shells in the form of path-helper and /etc/path.d/, but that's run through the profile, which won't affect GUI applications.)
I'm not really trying to defend OS X here, other than pointing out that if you cut out the proprietary GUI stuff, it's basically just your run-of-the-mill custom UNIX dist. As a long time Linux user (I use a Mac as laptop, because screw trying to get Linux working perfectly on a laptop), I find everything to be an equal pain in the ass to deal with. systemd or launchd, X11 or windowserver, Finder, Nautilus, Konqueror or even Windows Explorer - They all suck. Pick your poison.