What is the point in adding danger and unnecessary difficulty just for the sake of it? it seems a few here are expecting our ships to behave like a space vehicle designed in the 1960's. We scoop from stars, launch 2000+ tonne ships from 9g worlds, regularly put the ships through maneuverers exceeding 70+g. The game is set in 3303, not 2017.
That's the thing.
The whole problem with re-entry is one of thrust.
At the one extreme, one way to achieve re-entry is to de-orbit really gradually.
The problem with that is it's hard to judge your destination accurately, it means you're going to spend a lot of time in atmospheric flight, generating heat as a result of friction (and you WILL need to do that because you'll have a lot of speed to scrub off), and there's also the possibility you won't re-orbit properly and you'll end-up back in space again.
At the other extreme, you can de-orbit aggressively.
The problem
there is, quite simply, that you are heading toward the surface REALLY fast and it's quite possible you won't have enough time to aerobrake properly before you splat into the surface.
Pretty much
every realistic depiction of re-entry will involve something between those two extremes - from an "extinction event" asteroid strike to a controlled spaceship landing.
And none of that should present a problem for the ships in ED.
All the ships in ED have enough delta-v that they can come to a dead-stop in position above a planet in a couple of seconds and they also have enough delta-v that they can overcome gravity effortlessly.
Even with "proper", KSP-style, orbital mechanics in place, landing an ED ship on a planet's surface should only ever be a case of de-orbiting (which is, apparently, just done by reducing the throttle to zero. You don't even need to do a retro-burn), falling out of the sky and then allowing our almighty thrusters to arrest the descent once you enter the atmosphere.
ED is, basically, like playing KSP with the "infinite fuel" cheat enabled.
That being the case, any difficulty that was created for the sake of gameplay would be rather contrived.
Landing on an atmospheric planet should be exactly the same as what we already have but with coloured skies.