The answers already given are absolutely right, but another more basic issue shows up in your last paragraph: just knowing that $\varphi$ and $\psi$ are not "equivalent" (whether this means that they are not logically equivalent, or equivalent modulo some theory, does not matter), does not mean that $\varphi$ and $\neg\psi$ are equivalent.
That is: if we know that $\varphi\iff\psi$ is not a tautology (resp. theorem of ZFC), this does not mean that $\neg(\varphi\iff\psi)$ is a tautology (resp. theorem of ZFC).
This might sound like a violation of the Law of the Excluded Middle, but it's not: this arises from the conflation of proof and truth. Since we're talking about provability (either by $\emptyset$ or by $ZFC$), that means that we're living in the context of a modal logic (specifically, provability logic; see http://sartemov.ws.gc.cuny.edu/files/2012/10/Artemov-Beklemishev.-Provability-logic.pdf): in addition to the usual language of set theory, we also have a modal operator $\Box$, meaning "is a tautology" (or "is a theorem of $ZFC$"). The point is that $\Box$ is non-truth-functional: the truth value of $\Box\varphi$ does not depend only on the truth value of $\varphi$.
Using the modal language, your last paragraph should read: $$\varphi,\psi\in\mathcal{E}\implies \neg\Box(\varphi\iff\psi){\color{red} \iff}\Box\neg(\varphi\iff\psi)\iff\Box((\neg\varphi\vee\psi)\vee(\varphi\vee\neg\psi)),$$ but the red biconditional (specifically, the left-to-right direction) is false: we can't pass $\neg$ through $\Box$. For a concrete example, consider the continuum hypothesis CH: certainly $\neg\Box CH$, but also $\neg\Box\neg CH$ - $CH$ is independent, that is, neither provable nor disprovable from $ZFC$. If we could pass $\neg$ through $\Box$, this would of course be a contradiction; and the statement "$\neg$ passes through $\Box$" is precisely the statement "the system of axioms we are dealing with is complete," which is nuked by Godel.