I strongly agree with this excellent summary by GrandFather. There is a basic problem with the OP's summary statement, and the update doesn't really correct it:

In summary, don't blindly follow the rules or be afraid to break them. Think for yourself and make sound judgements.

The problem is that, without noticeable exception in my experience, any 'hacker' who is tempted to 'break the rules' fails to possess the judgment necessary to evaluate the extent of his or her own wisdom (or lack thereof). Programmers are an arrogant breed, and we are often guilty of overestimating our own intelligence or knowledge base. Saying it in another way, while we may have a pretty good idea of what we know, we are rarely in a position to know the extent of what we do not know. Rules or guidelines are the safety nets of the developing world, which help us avoid pitfalls that we might not even see, or are perhaps dimly aware of. Personally, I suspect that the so-called legitimate reasons for breaking the 'rules' fall into two categories:

1. They illuminate an ill-conceived 'rule' or a guideline that is insufficiently precise
2. They illustrate the triumph of the developer's ego over his understanding

I don't like rules any more than the next guy, and sometimes it irritates me when people spout a generalized version of a rule that doesn't apply to my specific situation. But nearly every major disaster that has befallen me in my programming career has been the result of ignoring one of these best practices.