When Apple started allowing clones, it was a good idea executed just a few years too late. A year or two earlier, perhaps, when Microsoft was still relying on the truly evil Windows 3.1, having MacOS compete on the same level may allowed Apple some success in becoming a software-focused company (although history also suggests they'd have eventually lost anyway). The Mac clones, however, were released in 1995, and had to deal with the anticipation of, and then the release of Windows 95, the OS that made Microsoft's interface at least a good approximation of Apple's, but also gave Microsoft the big advantage of pre-emptive multitasking and memory protection, two things that would REALLY hurt Apple until the release of OS X six years later.
It was a failed experiment. Rather than helping Apple, it caused their profits to spiral even further, and in desperation the company made a deal with Steve Jobs, to get him back in the fold.
When Steve Jobs came back to a dying Apple, he oversaw two things that brought it back into profitability: killing the clone market, and releasing the (wildly successful) original iMac. Neither step would have been successful without the other.
Margins in a clone market are horrendous. I read somewhere that if a company gets two support calls about a PC they've sold, that's their profit on that unit gone.
Apple survives because of the synthesis of their commitment to the innovative physical design of their machines, and the support for their Operating System from a committed core of users (and switchers such as myself).
Take away the control they have from being the only people able to produce Apple machines, and they might "find a way to survive", but in the process they'd either become another Dell - selling good quality beige-boxes[1] at razor-thin margins and hoping volume keeps them afloat - or worse, they'll bet their future on their superior OS... and become another Be.
OS X wouldn't save them. There is plenty of available evidence that it is impossible for anyone but Microsoft to survive making non-free desktop operating systems. There are very credible rumours to the effect that OS X for Intel already exists, and continues to be kept in parallel with the PPC version in case Apple ever needs to switch chip architectures. But you won't see OS X for Intel clone boxen because to do so would be Apple stabbing itself in the back.
So, they'd have to become Dell or Be. They certainly wouldn't remain Apple, and they certainly wouldn't "be a better company for it".
And as a whole, the industry would be worse off. The industry _needs_ Apple. You can see that from how many laptops these days look like TiBooks, or the way XP adopted both a similar visual aesthetic to OS X and followed it in its emphasis on the "digital hub".
It must gall Steve Jobs that Apple isn't as successful as Microsoft. It must gall Bill Gates that Apple always seems to read the mood and needs of users better than they've ever been able to.
The industry needs a company that can, every couple of years, do something nobody thought of before (both generations of iMac), or put a great deal of polish on an existing idea (the TiBook, the iPod). To do this you also need to be able to spend a lot of money on R&D, which clone-style markets just can't pay for, and likewise you must have enough reserves to survive when your gamble doesn't pay off (the G3 Cube, the Newton).
So, in short, I stand entirely by what I said in my first comment.
[1] These days, beige boxes are more likely to be black. That doesn't make them any less beige-boxes.
