I think one problem is that the law also applies to pharmacists who own the pharmacy. And if you own the bookstore, you certainly have the right to decide what books to sell.
The flaw in your argument is in comparing the owner of the bookstore to the State, and as of yet, the State does not have ownership of the pharmacies.
"Manion argued that forcing pharmacists to fill prescriptions they believe violate their religious principles not only places those pharmacists in a moral dilemma but also violates the so-called conscience clause that allows those in the medical field to avoid performing procedures, most notably abortion, that they find reprehensible"