From the available randomized controlled trials we have there's no indication that low carb would be bad, almost every health marker improves just as much as, or slightly better than, on low fat diets.
I posted this in another thread:
A review focused on discussion of why low carb works:
In short-term and long-term comparison studies, ad libitum and isocaloric therapeutic diets with varying degrees of carbohydrate restriction perform as well as or better than comparable LF diets with regard to weight loss, lipid levels, glucose and insulin response, blood pressure, and other important cardiovascular risk markers in both normal subjects and those with metabolic and other health-related disorders.
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The metabolic, hormonal, and appetite signaling effects of carbohydrate reduction suggest an underlying scientific basis for considering it as an alternative approach to LF, high-carbohydrate recommendations in addressing overweight/obesity and chronic disease in America. It is time to embrace LC diets as a viable option to aid in reversing diabetes mellitus, risk factors for heart disease, and the epidemic of obesity.
Hite AH, et al. "Low-carbohydrate diet review: shifting the paradigm" Nutr Clin Pract. 2011 Jun;26(3):300-8. doi: 10.1177/0884533611405791.
A review looking more at actual outcomes of low carb studies:
Meta-analysis showed LCD to be clearly associated with significant decreases in body weight, BMI, abdominal circumference, systolic blood pressure, diastolic blood pressure, plasma triglycerides, fasting plasma glucose, glycated haemoglobin, plasma insulin and plasma CRP, as well as with an increase in HDL-C. LDL-C and creatinine did not change significantly, whereas limited data were conflicted regarding plasma uric acid.
Santos FL, et al. "Systematic review and meta-analysis of clinical trials of the effects of low carbohydrate diets on cardiovascular risk factors" Obes Rev. 2012 Nov;13(11):1048-66. doi: 10.1111/j.1467-789X.2012.01021.x. Epub 2012 Aug 21.
And a review looking specifically at very low carb ketogenic studies:
In conclusion, the present meta-analysis demonstrates that individuals assigned to a VLCKD achieve significantly greater long-term reductions in body weight, diastolic blood pressure and TAG, as well as greater LDL and HDL increases when compared with individuals assigned to a LFD; hence, the VLCKD may be an alternative tool against obesity.
Bueno NB, et al. "Very-low-carbohydrate ketogenic diet v. low-fat diet for long-term weight loss: a meta-analysis of randomised controlled trials." Br J Nutr. 2013 Oct;110(7):1178-87. doi: 10.1017/S0007114513000548. Epub 2013 May 7.