I refer to Alan Aragon when it comes to his take on "clean" eating.
Its a long article with lots of good info. Here is part of that article on TFAs.
Trans fatty acids (TFA) have earned a lot of bad press for their adverse effects on biomarkers of cardiovascular health [17,18]. However, some research indicates that not all TFA are harmful. A distinction should be made between industrially produced TFA via hydrogenation of vegetable oils, and naturally occurring TFA in dairy and meat . Vaccenic acid, the main form of TFA in ruminant fats, might actually lower the risk for coronary heart disease . Currently, there’s no controlled human research specifically comparing the effects of TFA with other types of fats on body composition. In any case, the fitness-conscious population has nothing to worry about unless they start indiscriminately gorging on fast food, cooking with vegetable shortening, and pounding loads of processed/packaged pastries and desserts.
So, basically when it comes to the idea of "clean" eating the picture really isn't all that clear and no single food or food type can be looked at in exclusivity. Instead foods need to be looked at as part of an entire diet.