Your experience was completely self-inflicted. Who knew pointing a loaded gun at your face and then pressing the trigger would result in injury? If you do a dirty hack (and you did, there's no uncertainty) then you deserve what you get. It's analogous to using some type of unofficial installer for software in Windows or OSX, and then being surprised when the installer screws with all the other software in your system while it is at it. Also just because a package/program *can* run in your OS - doesn't mean it is actually intended for your OS.
Packages without repositories is silly and in this regard Windows and OSX are the same. Repositories are set up explicitly for your OS - so programs and libraries will always be built and configured correctly. With repositories you do not need stupid updaters for each program (which, by the way you're entrusting your system to -- fucking retarded) and you do not need to worry about dependency location, management and updating. Also you can fairly safely assume programs in official or at least well managed repositories (like RPMFusion) are non-malicious due to initial inspection and continuous oversight - this is far better than Googling for random programs and then just *hoping* they're OK when you install them. The lesson is: stay within your package manager and trusted and maintained repositories. If you stray outside - expect to be burned. If some silly Ubuntu tutorial tells you to do something which disobeys this then don't proceed unless you're prepared to clean up the mess and manage the ongoing brokenness.
You mention half-baked uninstall - this is another thing that repositories and real package managers solve (simply making all packages "self contained" doesn't solve all problems) because you have a mechanism that is overseeing the installation and removal of packages and making sure that things go in and out cleanly and configuration being re-jigged - as opposed to things just being there one second and gone the next.