For those casual readers who aren't into Fate series, let me explain the context behind this chapter's info:
For a mage to use their family magecraft, they require a special "organ" called Magic Crest. This "organ" is a record of all the spells a mage can perform and this is transplanted, generally from parent to offspring, to pass down all magical knowledge to the next generation so they don't have to learn it all over again from zero.
The thing is that since the Magic Crest is a foreign object in the mage body, it will reject it and will cause pain every time the mage use it, however that isn't the case for Kanata.
In Kanata's case, it seems like his body was somehow altered to prevent him to feel that pain and, while this might appear to be a good thing for him, it's actually the opposite. Had he practiced magecraft constantly like an ordinary mage without feeling the natural response of his body to stop, his magical circuits would've exploded from the inside and he would've died in extreme agony.
Hence Tsukumo affirmation of it being twisted malice: Kanata's parents not only wanted him to die, they wanted him to kill himself by accident so they could keep their hands clean. That's also the reason why they told him to not use magecraft in front of his grandma, she would've realized what they were plotting and maybe she could've stopped them.