Took a look at the book whose link you sent (thanks for that!), and there are the problems in it that are unfortunately typical of the Fraser Institute:
1) The assumption that market forces are always right, like when on page 11 where the fact that Canadians pay for alternative therapies "proves" that they provide a benefit;
2) That the placebo effect is enough to warrant continued use without government oversight - without considering that proof that the treatment does no harm is something that such oversight necessitates;
3) Reaching a conclusion that brand names would increase and maintain standards to a greater degree because of "competition between certifying organizations" is one hell of a leap of faith: if there are conflicting reports, people tend to choose one and disregard others. This choice is also affected by the advertising done by the competing bodies, meaning whoever spends more wins.
This holds true with the proposed "certifying agencies" replacing licences as well. It would be very easy for such agencies to abuse their powers, as alternative practitioners are VERY reluctant to call out a method that doesn't work, for fear of closer investigation into their own practices.
The Fraser Institute also often (as in this report) makes the assumption that government regulation eliminates competition and societal pressure, which is simply not true. Both of those things are still in place, as can be witnessed by (for instance) the Maple Leaf listeria disaster.
The British Petroleum nightmare going on in the gulf is a clear example of the difference between government and corporate standards: the regulators that were supposed to safeguard not only the environment but also the worker's safety failed miserably because they were influenced by the company (coke and hooker party, anyone?) into relaxing the government regulations until they were at a level the corporation wanted. There is no reason to believe that corporations, without oversight, would do any better, and plenty of reasons to believe they would do worse.
The banking system in the U.S. failed horribly, and are still fighting any kind of oversight, whereas the one in Canada - with some of the strictest regulations in the world - had not a single failure.
The Walkerton tragedy was a direct result of failure by the government to regulate water consumption - the province had slashed more than a third of those people hired to do so from its payroll. Their Drinking Water Surveillance Program was shut down, along with provincial water testing labs, leaving municipalities to use their own budgets or sell off the responsibility. (The UK had privatized water supplies in 1989, and not only did profits increase, but hepatitis A did too by 200% and dysentery by 600%. This is considered a success by unregulated free market supporters.)
So no, I'm not a fan of letting businesses or corporations regulate their own industries without any government oversight, and this Fraser Institute report hasn't convinced me otherwise. Thanks for the link, though!