Wit's End, Ionic Spark, Madred's Bloodrazor, Hextech Gunblade/Bilgewater Cutlass, Sunfire Cape, and Thornmail are all items that provide additional magic damage effects to your character in one form or another. So why do the last two need to do true damage? Well first, let's think about the primary difference between those last two items and the rest of the items.
Sunfire Cape and Thornmail are defensive items (Although Wit's End is debatable, you can argue that the item is firmly half defensive, half offensive, and the damage falls under the offensive aspect of the item.), whereas the other items are offensive. Why does this mean that Sunfire Cape and Thornmail need to do true damage?
Well, in the case of the offensive items, the idea that magic shred or penetration is needed to maximize their use is not strange; it's no different than needing last whisper to maximize the effect of an Infinity Edge. Builds are created with this in mind, and if there is any problem with this line of thinking, it's that Malady currently doesn't completely fill the magic penetration needs of an on-hit build.
As for defensive items, doesn't it seem a little off that an offensive stat, magic pentration, is needed to make either of these items really all that efficient? It doesn't help that magic penetration isn't a stat you want to invest in without investing in other stats. If I was playing an Amumu with Thornmail AND Sunfire cape, I would probably get almost as much damage out of a Rod of Ages (Plus the health and mana) as a Void Staff. Penetration is a great stat to amplify your offensive output; it's not a good stat to base your offensive output on.
Not to mention this completely gimps these items for non-magic damage characters. You can't even count on 10 magic pen from runes on someone like Darius. And yes, the idea that "not every item is good on every character" is certainly true for offensive items, this is simply not how it is supposed to work for defensive items; defensive items are meant to be useful against certain teams or characters, not necessarily on certain characters (Yes, some characters get slight amplification, like how thornmail is better on characters with taunts, but it's no where near as wide a contrast as how much better IE is on, say Graves, than it is on, say, Swain.)
So make these items true damage. If that was done they would 1. Be competitive as defensive items without needing magic pen, which is just a weird requirement to have for a defensive item to be competitive. 2. Choosing these items would be a bigger case of "Who am I going against" rather than "Who am I playing" which is how defensive items are meant to be picked.
So, without raising or lowering the cost, a reasonable change seems to me to be
1. Sunfire Cape's 40 magic damage is replaced with 30 true damage.
2. Thornmail's on hit reflect is changed from 30% magic damage to 20% true damage.