
I'm sure there are people out there who wonder why the heck freezing Megatron in ice actually worked.
I think it's like THIS...
You've heard of hypothermia, right? That's when your body temperature drops to the point where your body literally shuts down. I was thinking, did something similar occur with Megatron? Maybe what happened to him can be compared to that, in that temperature extremes aren't a good thing.
Everything I know of has a specific temperature range at which it functions best, a broader range at which it functions period, and anything outside that it won't work at all. If it's sufficiently cold out, it's hard to get your car to start. My grandparents experience that a lot (lousy northern USA winters...). If it's colder than that, your car won't start at all. So we can safely say that temperature has an effect on mechanical things.
When the ice broke under him (as the prequel comic clearly shows) and he fell into the water, it must have lowered his core temperature to the point where his systems involuntarily shut down. Maybe it was how fast the temperature changed, or how much it changed, but the result is the same: a major drop in temperature.
Now, for an organic being, if your systems shut down you're dead. For a mechanical being, shutting down is simply that. Remove whatever caused the shutdown and you're good to go, hence Megatron immediately waking up once the cryogenic thingamabobs shut down.
In case you're wondering why flying in space didn't have that effect on him, he travels in his jet form, and his jet form was designed for this kind of stuff. Logically, that would mean insulation where insulation is needed. But when he's not in his jet form, he doesn't have that going for him. No insulation to protect him from the cold.
And I'm not even going to TRY factoring in water pressure and whatever effect ice crystal formation has on circuitry...