As much as I support the renaming of 20th century US military installations such as Bragg and Hood, I agree with the decision to preserve the names and monuments at VMI. Hood and Bragg had absolutely nothing to do with the history of their namesake installations or the battles in which US soldiers fought after passing through their gates. Stonewall Jackson had EVERYTHING to do with VMI. I read Gen. Peay's entire letter. It is excellent. He obviously listened to and engaged with a variety of stakeholders.
The result, if Gen. Peay is able to execute as well as he can develop a plan, will be a preservation of VMI's Civil War History, including and especially the Battle of New Market, without turning it into the focal point of its entire history. One would hope that the likes of George Marshall can be seen as integral to VMI's history as Stonewall Jackson; the former being infinitely more consequential to the US and world and the later being specifically consequential to VMI's very foundations.
As a side note, I completely get the zeitgeist of VMI. Virginians, notably my Grandmother's family, saw their state almost as a country and culture unto itself. I remember visiting Lexington, VA as a child and visiting Gen. Jackson's grave. I can tell you that if Gen. Jackson was a "staunch Christian", as Gen. Peay suggests, it was mostly attributable to his 2nd Wife, Mary Anna Morrison, my Grandmother's great Aunt. My sister's first and middle names are Mary Morrison and its not coincidental.