As stated one of my earlier posts (specifically
Advice and Trust [NGE]), Yui's actions would be best framed as not psychotic or crazy, but as desperation.
Let's take a step back and look at the chess masters behind the whole shebang, SEELE. They as far as we know hold all the cards, or at most a great deal of the cards to Third Impact. They have the Dead Sea Scrolls, They have agents and hitmen at their beck and call who can make people disappear
easily (See Yui say as much in Episode 21), They have control of all the other MAGI Computers, They have the EVA Series, They have control of the JSSDF (And most likely many other Armed Forces around the world), and they have both physical body of ADAM (Prior to Gendoh taking it for himself and surgically implanting it into his hand/eating it) and the soul of ADAM in Kaworu amongst all other things... oh and they're rich as well. So in short, they have the foresight, manpower, and pockets needed to get
whatever they wanted.
Now imagine if Yui stopped the plans to Instrumentality
early, as in,
before Third Impact was well underway and SEELE was turned into goo. What would happen? You'd have a pissed off SEELE and a NERV that is WOEFULLY outgunned and at a severe disadvantage. Sure, they could ROFL stomp the JSSDF (or any other Armed Forces joining in as back up) using Unit-01 (which let's not forget didn't ingest a S2 organ this time around, that honor goes to Unit-03 thanks to Bardiel), but there's still the virtually invincible EVA-Series with the Lance of Longinus Copies... and SEELE has been at this since the medieval era if the Classified Information of Evangelion is to be believed. What
would be the sane answer to stoping a for all intents and purposes omniscient secret organization with control over the world via the UN?
Any plan Yui would have to concoct to stop SEELE would have to essentially involve taking them all down in one shot... otherwise NERV and the world would have to deal with a pissed off SEELE for years to come.... or the world could devolve a world-wide conflict versus rival nations and their EVA's and Werewolves...lol. But I digress.
Yes, Yui might not earn Mother of the Year, but put her decisions into perspective and remember who she is dealing with. Yes, the EVA's were made to stop the Angels, but this is only to serve in furthering the end game that is Third Impact. What better way to throw a monkey wrench into that plan then being the resident soul in said plan's lynchpin? In other words, she made a hasty and desperate choice because of the threat SEELE poses to the world, because she was both short of time (again, Episode 21 all but confirms SEELE was threatening her life if she didn't follow their scenario) and because she loved her son enough to sacrifice being there for him in person so that she can protect him in the form of EVA-01 when SEELE began the process of kick-starting Third Impact.
