Isn't the allowance of 'cronyism' etc, what makes the market "free?"
The original concept of free-market economics, as envisioned by Adam Smith, was defined in opposition to entities governments and guilds using their power to impose artificial rules in the market to subvert natural market forces like supply and demand. Pharma companies use regulatory capture to do exactly that: they set up a legal landscape for their own benefit and everyone else's detriment. Rent-seeking is anything but free-market.
So if I’m understanding correctly, the problem is not a lack of willingness to break up/regulate this monopoly, but instead the regulations and lobbying that explicitly facilitated its creation?
Are there any inherent facets of a free market that prevent such abuses?
It's incredibly hard to generate the political will of many people who will slightly be hurt by something against the will of the few who will be significantly hurt even if the aggregate damage is far greater for the many than the few.
Almost all legislation follows this sort of calculus: zoning laws, tariffs, minimum wage, etc.
No, there's nothing about free market which will automatically mitigate this issue. Markets are very good at certain things, like delivering goods and services efficiently if certain conditions are met, but they are not some panacea which can magically solve every problem.
There are certain cases where markets are not very good at serving a majority of people: for instance in the case of monopolies, or when there are negative externalities which are not priced into the market (for instance it can be profitable for a company to burn a lot of fossil fuels to produce products cheaply, and everyone else suffers the environmental costs).
Strict libertarians will disagree with me, but markets alone are not enough. In every example of what we could consider a well-functioning society, the government plays a role in guiding and constraining the market where necessary.
Regulatory capture does represent a problem, and is an example of bad government, but that does not negate the need for good government.
This is a natural and obvious end following from the foundation of capitalism, which is the existence of private property ensured by the state.