Entrepreneur Jeffrey Aronin said a few years ago he hoped to eventually sell Marathon Pharmaceuticals LLC, which he controls and runs, for billions of dollars, according to a person who heard the comment. Some employees have said they now expect him to shut down the company.

His deflated ambition is a sign of the increasingly hostile reaction to drug companies that specialize in sharply raising the prices of old medications. Mr. Aronin did that over and over again for 15 years, most recently after Marathon won approval in...