I just read in Prevention magazine that a study only one month long (and of only 18 total participants) Atkins raised LDL cholesterol by an average of 16 points, the Ornish plan reduced LDL by an average of 25 points, and South Beach reduced by 10.

This is only one study, and the study group was awfully small, and awfully short. It's possible that the effects a month later would have been entirely different (in either direction). The reported results also only consider the average, not whether some people on Atkins had substantially reduced LDL and some people on Ornish had raised LDL. Or, whether the rise in cholesterol had health implications, as I've also recently been reading that more studies are showing that cholesterol levels are a very poor predictor of heart disease EXCEPT in certain individuals (primarily those with diabetes, pre-diabetes/insulin resistance, and existing heart disease). For example, I believe it's the French who have cholesterol levels much higher than in the US, but a much lower incidence of heart disease.

I think there's no substitute for common sense and medical supervision. I believe that except for the very most extreme diets (like the ******* extreme combination of nearly no carb/no fat which can cause very rapid "rabbit starvation"), health effects are going to be gradual, so trial and error is a legitimate and safe way to monitor the effects of any diet (or any behavior change for that matter). So, if you see your doctor and have your blood drawn regularly (for me, every three months) you can discuss any changes and assess the risks with your doctor.

As with anything you do in life, there are risks and benefits. You have to identify and weigh the two, and decide which is best for you. It really doesn't even matter what is true for "most" people, if it isn't true for you.
For me, I really don't seem to be able to lose weight any other way, and I believe the risks of being over 200 lbs overweight are a lot greater than following a lower carb diet under medical supervision. If at my next checkup, there are issues like raised blood pressure, blood sugar, cholesterol... then I will discuss the risks/benefits with my doctor and we re-evaluate my diet and "tweak" it, if we feel it's necessary.