I don't know which option would be "better" for your chances. What's probably most important, though, is to get some good experience @ a job you enjoy. If it's science, that should include as much self-directed research as you are capable of, hopefully leading to publication. If you're looking @ pharma, though, my experience has been that the opportunities for publication are much more slim b/c of intellectual property issues.
Maybe it's b/c they rejected me
, so I'm a bit biased, but I'm just curious why you assume that Merck is a top-notch pharma company. Though their dominance in the '90s is unquestioned, I feel they've used that attitude to justify a bit of, shall we say, snootiness in their hiring that is no longer warranted given Vioxx & the uncertainty in their pipeline. They definitely do hire BAs, though.
Don't know what part of the country you're from, but the universities in NYC like Columbia & Rockefeller are very open to hiring recent graduates for biomedical research, knowing that you're thinking of going back to school. Anyway, lots of luck!