I always get confused when I try to use binding energies directly, partly because of the sign issue, and partly because differences in binding energies show up in the third or fourth significant figure. My favorite reference instead lists for each isotope a "mass excess," which is the difference (in energy units) between an observed mass and the naïve mass of $A$ atomic mass units. For beryllium and helium we have
\begin{align}
\rm\Delta({}^8Be) &= \rm 4.9416\,MeV \\
\rm\Delta({}^4He) &= \rm 2.4249\,MeV \\
2\cdot\rm\Delta({}^4He) &= \rm 4.8498\,MeV
\end{align}
This makes it clear that a $^8\rm Be$ is heavier than two $^4\rm He$ by about $0.1\,\rm MeV$ — it has more excess mass.
So what was wrong with your binding energy approach? You have
\begin{align}
\rm BE({}^8Be) &= 56.49955\,\rm MeV \\
\rm BE({}^4He) &= 28.3\rm\,MeV &\text{(careful with precision here)}\\
2\cdot\rm BE({}^4He) &= 56.6\rm\,MeV
\end{align}
Here you have the same energy difference, about $0.1\rm\,MeV$, but it appears to go the other way, as you point out in your question. That's because helium is more tightly bound than beryllium; when beryllium-8 fissions, the extra binding energy is released.