The speed of light, $c$, is also always expressed in units that are fundamentally "arbitrary", that is, they're a matter of convention. So there's no problem, if you choose other "arbitrary" units to express your masses and your energies, the ratio $E/m$ will still have units of speed squared!
A way to see this, is to express the quantities via the more general technique of "dimensional analysis", which doesn't commit to any specific choice units. We know that:
\begin{align*}
\text{Energy} &= \text{Force}\times\text{Length}
\\&= \text{Mass}\times\text{Acceleration}\times\text{Length}
\\&= \text{Mass}\times\text{Speed}\times\text{Time}^{-1}\times\text{Length}
\\&= \text{Mass}\times\text{Length}^2\times\text{Time}^{-2}
\\&= \text{Mass}\times\left(\frac{\text{Length}}{\text{Time}}\right)^2
\\&= \text{Mass}\times\left(\text{Speed}\right)^2
\end{align*}
which I have written in this jarring notation just for the sake of those less familiar with the shorthands for the basic dimensions (MLT - Mass, Length, Time).
Anyway, the above shows you that mass is related to energy by a factor of speed squared, and that is true regardless of the choice of units.
A separate thing is, that in the rest frame of a mass, we have exactly $E=mc^2$ with $m$ the rest mass. There are many, many posts here about why that equation isn't always true if $m$ is not at rest, and various historical aspects leading to that equation still being so famous. See for example this post.