If you really, really wanted to do a direct measurement of the separation energy (instead of doing precision mass spectroscopy), you could use the
"shooting protons from a cyclotron at the $^{56}\mathrm{Fe}$ atom[s]"
approach.
But for practical reasons you would not look for the lowest energy at which you start getting neutrons out (which I would described as "direct threshold detection").
The practical difficulties with direct threshold detection are two:
The cross-section rises from zero at threshold. So there is always a vanishingly small rate near threshold.
At threshold the created neutron will have zero momentum in the CoM frame meaning that (a) in collider mode it leaves the interaction zone (if at all) with very little momentum making it extremely difficult to detect and (b) in fixed target mode it goes straight down-stream and lands in the beam-dump undetected (you can't use a 4-pi detector for this because your production rate is extremely small due to item (1), so you need a high-current beam).
What you do instead is use a variable beam energy above threhold but perform an exclusive measurement and reconstruct the neutron's CoM kinetic energy $T_n$ as a function of beam energy $E$. Then fit to find the threshold energy
$$ E_\text{th} = \lim_{T_n \to 0} E \;.$$
This means that the rate is non-triviall and the ejected neutrons are energetic enough to deviate from the beam direction and arrive at a detector with enough enegy to be easily detected.
It is an entirely practical measurement, but it won't give you the kind of precision that comes from mass-spectroscopic methods.