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I'm not even sure I'd say there was magic in it initially.
At no point is there any mention of the markings themselves (in The Skinsaw Murders or even in The Hook Mountain Massacre) being magical. The rune is certainly a focus or component of the spell or ritual used to harvest souls, but that doesn't make it magical. And as noted above, if there was magic in the markings, it would have been expended with the subject's death. And unless the original magic's power was Overwhelming, the lingering aura left by any such magic would be long gone by the time the PCs arrive.
It's not magical per say, but it's part of a ritual, so it should be able to be identified as such on a good enough Spellcraft check, especially if your party's spellcaster is a Conjurer or Necromancer and took his time to examine the runewell at the catacombs of wrath (unless you go for the railroad-device built in the adventure and make rune magic impregnable, I know I didn't).
Is the pinch of sand used in a sleep spell magical? No. But it is needed to cast the spell.
Think of the rune as a replacement for a magical component (or even a verbal or somatic component). Nothing more.
So no... It does not radiate magic.
(The easy way is always the best way... In my opinion, of course)
Ultradan
The Sihedron Rune is no more magical than a pentagram or the number 4 or the letter B. It's just a symbol. That said, it's certainly a common symbol in Thassilonian writings, since it's basically the symbol for "magic" in their language more or less. So it'll show up a lot in magic books or on old scrolls or other magical items, but the symbol itself is not magic. Unless it's part of something like a symbol spell, I guess...