Apple tried to allow clones, but ran into the same problem because the clone makers could make cheaper machines by slapping together parts.
Yeah, this is exactly what happened, although some of the clone brands were perfectly high-quality (Power Computing in particular made great machines, usually the fastest on the market). In the Mac community at the time, a lot of people (myself included) wished Apple would just exit the hardware business and focus on what they were good at: software.
Then Steve Jobs came back and did exactly the opposite of that. First order of business was to kill cloning. Then came the iPod.
To be fair, the next generation of Power Macs after that were about half the price of the previous gen.