Not voting in this, but an observation that I haven't seen anyone make yet. Konan is a chakra entity at least 150 metres across who can control paper - including paper seals - in her radius. Orochimaru explicitly warned us that she uses this to assemble and activate seal arrays on a battlefield timescale.If the countermeasures are fuinjutsu related, then it's either Itachi, Konan, or Sasori doing it, in increasing order of likelyhood. If it's jutsu related, then it's probably Konan, Kisame, or Itachi. If it's both, then that more or less leaves Konan and Itachi.
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3) How Exactly
So, are the countermeasures ninjutsu or fuinjutsu? I would think that it would be quite difficult to pull off a general purpose summon popper jutsu, that seems like it would be so horrifically unbalanced that the setting constraints would essentially demand that it be impossible to craft. Perhaps in a limited form a jutsu would make sense, but I interpret "meaningful countermeasures" to mean that this is something that can be deployed at battlefield-scale and without much effort in the moment, or could otherwise be prepared on site in advance. I would think sealing would be the better option there, since the chakra diffusion effect is a thing.
Naturally, this is not solely a disrupting tool. She rapidly arranges and activates seal arrays mid-combat. She is a jōnin-level sealmaster and consequently has access to a variety of tools. If you recall my note on her intelligence, you will understand why she is exceptionally deadly as a result.
It would surprise me quite a bit if Akatsuki had a seal array that could destroy Summons over massive ranges. It would surprise me a lot less if Konan had some kind of seal array covering one or a few Zones that pops summons who are inside it when activated. Her time is limited by the fact that she acts as Kage of Rain - but we have no idea how much multitasking capacity she has, so that might not be a true limitation for her.
It's also worth noting that Oro described Konan as:
Given Orochimaru's notoriously low assessment of our Sealing skills, I'm going to read that "perhaps even my equal" as "at least an AB higher than me" (given that we've never heard of Oro being especially focused on TH that I recall); Konan sounds like she has TH in at least a 70-slot, maybe higher, enough that the rules the rest of the setting has to follow about what ninjutsu can and cannot do may not meaningfully apply to her. It certainly seems possible that she could design custom techniques intended to work with a seal array she knows how to make.She is quite the genius of ninjutsu creation and perhaps even my equal in that regard. However, where I have spread my attention amongst the elements and beyond, she has focused single-mindedly on her paper-style ninjutsu. She has several particularly lethal tools as a result.