50-nvidia.conf is part of the nvidia packages, so it should be removed when you uninstall the packages.
And booting to recovery mode should have worked in any case I think.
Unless you use GNOME. But even then you should have been able to login in text mode.
Anyway, I take it your problem is solved now?
And I hope you uninstalled the nvidia packages before you installed the driver manually. Otherwise some files will be overwritten when there’s an update to the packages, which will cause you problems again.
Please note, that when installing the driver manually, you have to reinstall it after certain updates (kernel, Xorg, Mesa).
I must admit that I’m not 100% sure, but I’m pretty confident that kernel modules are loaded always, as they are the requirement for everything else in the system.
But that file doesn’t tell the system to load the kernel module.
It rather changes some parameters in case the module is loaded.
Recovery has a lot of failsafe kernel options. Those might prevent the nvidia from being loaded. At least they do seem to prevent the fglrx kernel module from being loaded, as I saw in a different thread in the german subforum recently where somebody had problems after installing fglrx because the kernel module was not loaded as he had the “acpi=off” and “apm=off” kernel options on the normal boot’s kernel command line…
I haven’t figured out how to blacklist a specific module through grub.