I'm pretty sure they've always been behind the checkout counter. Most (all?) stores that sell smokes keep them somewhat guarded to prevent people (particularly minors) from stealing them.

The only thing in the pharmacy proper are controlled (mostly prescription, but their are a few non-prescription pharmacy-counter-only) drugs.

Cigarettes aren't in the pharmacy area of my local CVSes, they're at the front of the store behind the regular cashier.