Is there a legal difference between using pharmageddon or the implied meaning of the word pharmageddon?
It depends on the context, wording, and substance of the "implied meaning". If these are in the sense of the comments to your question, then there is no difference from a legal standpoint. The lawfulness of both alternatives is premised on the First Amendment, which protects free speech. Many other countries have in their legislation or Constitution equivalent provisions to protect the freedom of speech.
Here, the invented term pharmageddon constitutes rhetorical hyperbole. A reasonable person would understand it not as a concrete entity controlling the medical schools, but as an adaptation from the Book of Revelation to give a connotation of doom or catastrophe in the context of medicine academics.
The statement of fact "[A] numer of medical schools are run by pharmageddon" would not be actionable as defamatory because it does not sufficiently identify entities (such as specific pharmaceutical companies and/or medical schools) of which reputation is or could be harmed by that statement. Even if the publication singled out specific entities, actionability would depend on the veracity of the notion that the denounced dynamics hinder the schools' priority (i.e., academics & research in medicine) and/or the righteousness the allegedly controlling entity is expected or required to maintain.