I know two people this story could easily apply to and for both of them that's not at all paranoid. Both of them have had the resources of various nation states thrown at them on multiple occasions and they are both still walking the earth last I checked.
To describe this as malignant would require you to be intimately familiar with everything they've been up to. There was a short period where I myself had very good reason to be that paranoid (and more, in fact) and it's not a memory I like to revisit much. Being paranoid is one thing but to actually know that you may be - for whatever reason - a legitimate target changes things considerably.
What do you have to do for "nation state sending ground operatives to do hardware-level attacks against your security" becomes part of your threat model as an academic?
He was was an armchair cryptographer. Not a particularly bright or studied one, but a cryptography enthusiast nonetheless. The kind of person to get all hand wavey about the efficacy of timing attacks and POODLE.
To describe this as malignant would require you to be intimately familiar with everything they've been up to. There was a short period where I myself had very good reason to be that paranoid (and more, in fact) and it's not a memory I like to revisit much. Being paranoid is one thing but to actually know that you may be - for whatever reason - a legitimate target changes things considerably.