I wasn't aware we subsidized Walgreen's, Rite-Aid or CVS. That said, ending our paying for the R&D of the pharmaceutical companies while other countries don't is something we need to address and have for a long time.
CVS at least is. I work for a CVS branch that is funded by the government.
And to answer the question, if the R&D isn't subsidized, we'll just end up paying for it some other way. Either through when Medicare/Medicaid pays over a $1000/pill for new drugs because that's the only way the company can possibly make a profit before generics hit the market and undercut it, or in subsidizing insurance companies to do the same thing. This is a sector of the economy where the old mantra of "let the free market take care of it!" simply won't work, unless patent laws are changed drastically, in which case there would be a far bigger threat from the Martin Shkrelis of the world.