A bit of a rant ahead, but I am really tired of people still treating Linux like it's 1997 or expecting it to work like their old OS did and then running into silly problems that none of us, who actually spend our day in Linux, run into.
These problems sound more like inexperience in using Linux to me than anything else. fsck works automatically after a power failure, configuration doesn't override itself and installing a package from the web, while not a great way of doing things, definitely does not prevent you from installing other packages, unless you somehow broke a whole lot of other stuff by deleting dependencies without really understanding what you were doing.