I think it was done appropriately to indicate the dark tone that was going to be taken. No point lying about it, military troops have done some horrific things already with prisoners in real life that aren't sanctioned or orthodox. It's a tough topic to tackle but it's totally in line with the sort of 'anti-military' theme Metal Gear games gun with.
It does set Skull Face up as a horrific monster but again I don't think it's entirely inappropriate given the specific situation Chico and Paz were in. If they'd played like a tape of IT happening then sure I'd say that would be unnecessary and absolutely not ok but they left it implied and off-camera so they have some degree of sense.
Also regarding the existence of the tapes, some were legitimate recordings by Chico to warn Big Boss and detail his infiltration. The rest, I believe it's revealed in another tape, were made by Skull Face for Chico to listen to in order to remind him of what he did and what happened in the torture sessions.