I finally got back into this game this weekend and just beat it. Whew!
I played through most of the game stealthily. Some sections can't be stealthed, and some segments I just said fuck it and blew everyone to pieces. The game wasn't really made for stealth, but it's kind of nice to have only a few tools at your disposal (hatchet, silenced pistol, and leaning from cover). It plays like a very simple stealth game and it sort of works in most segments, because there's actually few enemies that spawn and they aren't very perceptive. Once someone finds a dead body though, they all go into alert mode and can spot you from a mile away. And some sections just have too many enemies to reasonably stealth through. But for the most part, it's surprising how few enemies there are if you don't alert anyone, and how few enemies you actually have to kill. I'd say other modern stealth games have higher enemy counts, because they also give you more tools for dealing with multiple enemies while staying stealthy.
I guess the next thing to do is the Uberkommandant missions. It sounds like these missions have alot more heavy/armored enemies, which doesn't bode well for a stealth playstyle. But whatever, I'll give it a try.