The church does emphasize (careful) secular education. But I think the original comment was referring more to doctrinal education, which the church actively discourages. Also, if doctrinal education ever conflicts with secular education, then doctrine trumps everything.

The example of the money the church pumps into BYU does more to hurt your counter-argument than to help it. The church pumps so much money into BYU so that it can provide formal education to its members, while controlling the education experience. The purpose of BYU is exactly to further the controlled church experience and controlled education of the world.

In fact, the Church is incredibly smart in how they operate. The most personal interaction you have with the church is between the ages of 18 - 25. These are the most malleable ages for a young adult, since this is the time that they naturally seek direction and purpose in their life. The church is top of mind for members during this time, and so the church has created a system where they can control these important years to mold future faithful followers and spread the religion.

The day you turn 18 they start "preparing you for a mission". Then they send you to the temple where you are told that you have now entered into covenants that, if broken, will now fuck you up for eternity. With the fear of your eternal salvation in the balance, they then send you off for 2 years to a church obedience boot camp (usually referred to by the euphemism of "a mission") where they literally control everything you say, think, or do for 2 full years. They pull you away from the environment you once knew, even frequently to another country. They control who you associate during these years, and try to build habits towards being a good future member. As soon as you graduate from the 2 year boot camp, they promise a sex-deprived 21 year old that they can now get laid by going to BYU and finding a beautiful mormon virgin who has been waiting for them their entire life. Then at BYU they can again control the narrative of your life. Curriculums meet national standards for accreditation here, but are also taught by other members who are committed to controlling the narrative of the Church. Now that you are married, you are encouraged to start having kids. Most BYU grads will already have kids by the time of their graduation. Once you have kids, now the emphasis is to raise them within the church. They will now begin primary school (as you once did) and continue the cycle that you just completed. By the time the church "lets go" of you during this important part of your life, you are 25 or 26 years old, already have several kids, and you don't want to ruin their lives by questioning church teachings. You final job as a 26 year old member is to "endure to the end". Quite possibly the saddest, most depressing stage of Mormonism. I hate when my Grandma tells me she is "enduring to the end". During this stage (between ~30 -> death) your goal is to "endure". Not enjoy, but endure.

During the endurance stage you are told to: go get a job so you can pay for your kids and pay your 10% of your pre-tax income as "tithing". Go to church every sunday. Take your kids to church every wednesday. Go to the temple for further doctrine reinforcement on Saturday. Don't drink coffee, tea, alcohol. Don't think impure thoughts. Just rinse and repeat. Just "endure", until you have the pleasure of dying.

BYU is very important to the Church's membership and tithing dollars. They aren't running that church from the bottom of their hearts. It all controls their members. If you remove BYU from the church's plan (as outlined above), they would lose MANY MANY members during those important ages of 18-25. They have created an effective algorithm/strategy that creates a cycle of promises and control mechanisms to keep you in the hamster wheel. BYU is critical to that strategy. That is also why BYU Idaho exists. It allowed them to broaden their net to even more young adults.

This is mostly the controlled experience that a man would experience within Mormonism. Unfortunately a woman's experience is even more depressing and controlled. But follows a similar outline.

So back to the original point. Yes, I would argue that in fact, "The Church of Jesus Christ of Latter-Day Saints actively discourages any sort of rational individual thought".