Role playing games is supposed to be about having fun. Saying that "house rules ruins game forever" makes no sense, because if house rules make YOUR game more fun, then it is a success! It may not be a success in the part of the publisher, but it definitely is a success in the part of the players.
Rules are there to provide common ground for everyone. They're supposed to allow to to know what to expect from a certain action. If a game gives me the option to raise a "hit with sword" skill and a "shoot with magic wand" skill, it's because it wants to allow me to define what my character is good at. If a DM rules on-the-spot "roll your sword skill to hit with wand!", I'm going to be upset, because I was tricked into thinking that I had to invest in the wrong skill.
But if a rule detracts from the fun and everyone can agree that it should go away, then what's the problem? Unless you're in a RPG tournament (whatever that means) with standarized rules (don't they ALSO have standarized HOUSE rules?), who exactly is harmed if you decide to, for example, do away with Skill Challenges as written in the 4e Manual, and roleplay the entire event, rolling once or twice to pass a skill check maybe if the DM thinks it's relevant?
MANY roleplaying games actually tell you to use this rule, or that other rule if you like it better (GURPS for magic, for example.) Or use the advanced rules, if you want extra detail. Or pick and choose WHICH advanced rules you want to use and which you don't.
If players complain because the DM decided to gut the entire Leadership (?) powers from the book, then that is their right (specially those who have rolled Clerics or wossname... warlords). If players are ok with the DM only allowed one extended rest per session, or unlimited uses per session of magic items, or decide to include wands with limited charges, what.exactly.is.the.problem? There doesn't even need to be a rule, just flavor text: this item will only work a few (x) times before it runs out for good.
Complaining that a game has rules that make it seem like a computer game, and then complaining that players are like computers because they follow rules blindly... I mean, seriously WTF? I thought that what made P&P roleplaying games BETTER than computer roleplaying games was that the computer can't do anything it hasn't been programmed for beforehand, but a DM can improvise?