Why is this a disaster? My 10 year old son has been doing this for years without any problems. It has encouraged him to start poking around other game parts and learning lots in the process.
Edit: There are also many easy to use front ends for adding mods and working with different minecraft versions etc.
* Because your patches only work against one version of the game.
* Because you are directly updating files, so both of the previous restrictions can easily be violated, which tends to cause a crash on startup.
The front-ends work around this lunacy by keeping multiple clean copies of the entire install, at multiple version levels, so that each mod can trash it on its own or use the version it needs.
Edit: There are also many easy to use front ends for adding mods and working with different minecraft versions etc.