On the other, and I speak from experience, we really don't fully understand what goes on in terms of gene expression regulation. We have ideas which generally work in vitro, mostly in vivo with model organisms (drosophila, yeast, etc) but relatively little basic research looking at fundamental mechanisms of regulation is done in higher eukaryotes. The upshot is that we may have ideas of what's happening, but those ideas may be one of several possible explanations which lead to similar outcomes. Moreoever, the impact of gene therapy in terms of a long term cellular (and immune) response is poorly understood.
I'd be intrigued to see what longitudinal data have been generated to show Glybera's safety over the kinds of timeframe relevant here.