They represent different terms in Economics, and often questions of utility type (welfare, differentiation) are different from those of preferences (risk aversion, non-homotheticity).
I see no reason for a merger.
Merging seems rational in most cases but as you point out the two tags are not always interchangeable. Is it that much trouble to apply both tags? Right now there are 16 questions tagged as preferences and 34 tagged as utility. Even manually editing questions from others seems doable.