Fantasy/ magic games are always interesting because there's resurrection spells, therefore the argument can always be made that death has far less consequence.
Need a marginally intact body and spirit/soul/life force to resurrect someone in AD&D (and plenty of other fantasy systems/settings)...and these CRPGs also allowed things like death spell (which blasts one's life force out of existence), disintegrate (turns one's body to dust and scatters it), or shattering of frozen or petrified people. These rules even applied to player characters on the core rules or harder settings...a character takes an extreme form of damage and they don't just die, they are forcibly removed from the party, forever.
Irenicus gives a good demonstration of some of these effects when he escapes Spellhold in the second game:
First two guys are hit with death effects (plus plenty of overkill, including disintegration) and the last...well, maybe if the janitors find enough of him and someone's got a lot of tape.
Depending on one's views regarding an afterlife it could be argued that, in fantasy settings like these, the consequences of some forms of death can be more severe. A real-world follower of any of the Abrahamic religions, for example, is likely to view the soul as eternal and some form of afterlife a guarantee (even if it's not guaranteed to be pleasant). In AD&D there are many ways to not only render one's foes permanently dead (barring something like direct divine intervention), but to deny them any kind of afterlife as well.
But i think it's the 3rd person view and low detail aspects that probably make them "ok"
I never played deus ex... it looks very "goldeneye" in its level of detail. It's also a 2000 release, which although there were plenty of video game controversies before then, was before GTA 3 which drew a lot more attention into this sort of thing.
I'm sure censors have become more picky over the years and that graphical fidelity also plays a role...which has been something I've always found rather odd as it's clearly not gore that separates killing an active combatant and an unconscious individual, or an adult and a child, or an innocent bystander and an enemy.