You make very good points, and I think it's far from proven that alcohol actually is good for you or that raising HDL by itself is a good idea (in fact, there are some populations with low HDL but very low CVD). Probably another overlooked factor is the size of the HDL particles. Or it could be, as some people argue, that HDL is just a marker and so affecting HDL directly won't change your health.
Torcetrapib is complicated as a CETP inhibitor. The drug didn't just inhibit the conversion of HDL to LDL (which means it didn't just boost HDL, but it also lowered LDL), it also inhibits reverse cholesterol transport (where CETP is involved). Patients on torcetrapib had weird distortions in a number of blood values, increased blood pressure, and other effects. Which was the cause of increased mortality? It's too early to know, although it's pretty clear that CETP inhibitors are a bad idea.
My point was more that we have more than just correlations that people who drink alcohol have lower mortality and cardiovascular risk (observational studies often turn out to be misleading), we also have some somewhat plausible mechanisms for why this would be the case. It'll definitely be a long while before we can actually know whether or not alcohol has net positive or negative affects.