Don't go by "it's a scam" hits on the internet. That can often be the sign of posts by competing product salespeople (when their companies do not require them to be ethical), or by disgruntled former distributors who either didn't follow the plan or who engaged in unethical practices.
I am not an Isagenix distributor nor have I ever been, so I have no vested interest here. They are a member of the Direct Selling Association, which is a watchdog agency that only invites in reputable businesses after over a year of scrutiny.
It's not a pyramid - pyramids are illegal. They sell a product through individual distributors. Nothing different about those people trying to see to you and the local GNC trying to sell to you. They just don't put a ton of money into advertising. Nobody's going to make any money if they just sell you a 2 week supply of anything, so the better companies are looking for lifelong customers - and that applies to direct sales and supermarkets and "health food" stores and everyone else. Those that sell in public markets count on a lot of new customers to replace those who disappear after 1 sale (which is one reason why they advertise) and they also hope ads/marketing will make you think a product works and drive you back for repeat purchases. Direct salespeople know they will make no money on a consumable product if you don't keep coming back. And most economists will tell you that corporate America - the big companies - represent the true "pyramids" because the top execs make so much more money than the people toward the bottom who do all the work. So there's nothing inherently better about a company that sells through stores and one that sells direct - in fact, the ones that sell through stores have far more levels than the ones imagined by those who dislike "multi-level marketing" without knowing how it works. The disparity between the top and the bottom in direct selling is far less than in, for example, Walmart.
That said, I think there are very few products that "help you lose weight" per se. There is some research now about raising hormone levels of adiponectin and leptin that affect feelings of hunger vs. satiety, and that control FFAs (free fatty acids). I know of no clinical trials on Isagenix, and I know they do not contain this particular ingredient to raise those hormone levels to positively affect your weight.
There is plenty of research that says that better nutrition at the cellular level (not regular food!) helps cells function better and stop cravings. And certainly people who starve themselves do worse at weight loss than everyone else. So any "diet" product has to be nutrient-laden and it has to avoid stimulating the central nervous system - a lot are caffeine based and that's a disaster.
Doctors have been saying "eat right and exercise" for decades, and we have a greater weight problem as a country than ever. Two out of 3 people will die from non-contragious, chronic, degenerative diseases (cancer, heart disease, and diabetes). So it's more than diet, exercise, and drugs when those don't work! I could go on and on about our food supply and the nutrients our cells really need, as well as the work being done in nutritional epigenetics (which has been all over the news for over a year, and in scientific journals for about 15).
There are very few nutritional products that have clinical trials as well as patents (proving safety, effectiveness, and uniqueness). Be careful about claims. A lot of companies get in trouble for making claims that cannot be supported, and the FDA and the FCC clamp down on them. It's not just direct sales by any means - Activia yogurt and Airborne are 2 big ones that had to recall their ads.
So I would look into the background of any product/company I was considering, rather than make a decision at the outset based on how they sell.