The solution is stealth and aiming. A little practice with a scope will perfect the single head-shot takedown. Target location matters and opponents can take several arm or leg shots, but a surprise head shot is usually fatal. The levels are also well planned, with alarms for guards to sound and coordinated responses to intruders. Figuring out the patrols and avoiding trouble permits you to thin out the ranks of guards before facing them en masse.
Individual weapons are upgradeable with mods found throughout the game.
Use them immediately and try to concentrate mods on a few weapons you plan on keeping. Despite what the game's documentation suggests, each successive mod has the same effect. The scope mod lets you be a sniper with just a pistol, and the long range of the sniper rifle is rarely needed. The recoil mod is really only useful for automatic weapons. With a scope upgrade, you can thin out any guards silently and easily.