Clients seem to come in sets. A couple months back, I had several clients who had hired cheap off-shore companies 12 time zones away whose developers were curiously unavailable by phone, email or carrier pigeon. You probably already know the rest of the story: client needed to spend more money to have someone else go in and try to make it all work. (BTW, always use the term "refactored" rather than "threw out" when referring to the busted up stuff the client paid for).
Lately the theme has been clients who hired a 'Drupal developer' to do custom development and ended up with hacked up Drupal core, semi-working custom functionality and lots of odd behavior in different parts of the system. As an intelligent, hip, effective web entrepreneur, you should not strive for this.
Gumby -vs- Pet Rock
The typical LAMP application is made up of a tightly coupled set of code that all works in unison. While you may be able to configure this type of application, you cannot easily create or remove core functionality yourself. There is absolutely nothing wrong with this approach if you're developing a closed system designed to be maintained by a relatively small group of developers and whose feature set is pretty easy to anticipate and can be built in from the ground up. But this approach is not a good one for something like a CMS.
Why, you ask? Well, this is quite a coincidence as I was just preparing to answer that very question. Unlike more specialized applications (think phpbb, phpmyadmin, photo galleries, etc...), a good CMS is something that you should be able to extend, possibly in ways never imagined by the authors of the software. This type of extensibility separates applications like Google Maps from MapQuest. Like Gumby, Google Maps can be made to do any number of things never thought of by Google (from a developers perspective). And like a pet rock (did I just give away my age?), MapQuest pretty much does what it does, and if you want it to make it do something else, that's too bad, you should be using Google Maps, fool!