While the specific claim is exaggerated and doesn't support the argument for alternative medicine, there is evidence that a disturbing proportion of conventional medicine is unproven and wasteful
When I first saw the headline question I thought it raised an interesting and challenging issue for modern medicine. Then I read the Freedom Health Canada argument which seems to want to make a case for applying "alternative" medicine. So while they raise interesting criticisms, the argument that conventional medicine hasn't been proved to work so you should be prepared to try other forms of medicine that haven't been proved to work, isn't coherent.
But there is legitimate and skeptical criticism of much of what is done in the western medical establishment which is sometimes shockingly complacent when it comes to demonstrating the need and value of the treatments it offers. Some examples are given below.
A good review of some of the key issues is found in the recent books Testing Treatments and Better Doctors, Better Patients, Better Decisions. The first chapter of the second book starts by quoting two extraordinary examples where the US health system overuses screening in expensive and damaging ways:
Almost ten million U.S. women have had unnecessary Pap smears to screen for cervical cancer--unnecessary because, having already undergone complete hysterectomies, these women no longer have a cervix. [Original JAMA paper here]
Every year, one million U.S. children have unnecessary CT scans. An unnecessary CT scan equates to more than a waste of money: an estimated 29,000 cancers result from the approximately 70 million CT scans performed annually in the United States. [NEJM reference here]
While we tend to casually assume that medical treatment is good when it happens and when it doesn't happen it is because of rationing, that idea can be tested and that testing provides an excellent test of whether the treatment benefits patients in the first place. Natural experiments exist because the amount of specific types of activity varies widely in different regions of most countries. For example, the number of hip replacements per 1,000 people varies by a factor of more than 5 in different parts of england.
The most thorough analysis of such variation and the best analysis of the resulting cost and health gain for patients is found in the ongoing work of the Dartmouth Atlas Project for US healthcare (website here). Their work has uncovered vast degrees of variation in what activity gets done and has demonstrated that more healthcare is often worse for patients. In their own words (but my emphasis to show how their work is relevant to the question):
Supply-sensitive care refers to services where the supply of a specific resource has a major influence on utilization rates. The frequency of use of supply-sensitive care is not determined by well-articulated medical theory, much less by scientific evidence; rather, it is largely due to differences in local capacity, and a payment system that ensures that existing capacity remains fully deployed. Simply put, in regions where there are more hospital beds per capita, patients will be more likely to be admitted to the hospital. In regions where there are more intensive care unit beds, more patients will be cared for in the ICU. More specialists will result in more visits to specialists. And the more CT scanners are available, the more CT scans patients will receive. The Dartmouth Atlas has consistently demonstrated these relationships.
In regions where there are relatively fewer medical resources, patients get less care; however, there is no evidence that these patients are worse off than their counterparts in high-resourced, high-spending regions. Patients do not experience improved survival or better quality of life if they live in regions with more care. In fact, the care they receive appears to be worse. They report being less satisfied with their care than patients in regions that spend less, and having more trouble getting in to see their physicians. Most studies have found that mortality is no better in higher in high-spending regions, almost certainly because the benefits to some patients are counterbalanced by the harms to others. Hospitals can be dangerous places, where patients face the risk of medical error, adverse events, and hospital-acquired antibiotic-resistant infections. As more physicians get involved in a patient’s care, it becomes less and less clear who is responsible, and miscommunication and mistakes become more likely. Greater use of diagnostic tests increases the risk of finding -- and being treated for -- abnormalities that are unlikely to have caused the patient any problem. Patients who receive care for conditions that would have never caused a problem can only experience the risk of the intervention.
These examples show that much activity in conventional medicine cannot be justified by evidence. More detailed evidence could show that whole classes of activity are hard to justify, but the above examples are simpler.
So, though the original claim exaggeration is a failed attempt to advocate alternative medicine, there are legitimate and important reasons to be skeptical of the evidence base about much conventional medical activity.