Short answer: no. LearnToMod is only compatible with regular, vanilla Minecraft - both MinecraftEdu and Minecraft Education Edition have a setup that is not compatible with LearnToMod's software.
A few years ago, teachers who used MinecraftEdu had the option to download the vanilla minecraft launchers but MinecraftEdu is no longer available and neither is this option.
As you may know, Microsoft plans to phase out MinecraftEDU in favor of a new "Education Edition" of Minecraft.
As of April 5th, educators will No Longer be able to purchase MinecraftEDU. Read more about the transition plan for MinecraftEDU users here. However, educators who have purchased MinecraftEDU pre-April 5th 2016, and downloaded the vanilla licenses will continue to be able to use MinecraftEDU with LearnToMod for as long as they like. According to the MinecraftEdu website, they'll also get 1-year of the new Education Edition for free. Learn more on MinecraftEDU's website here.
Just as with MinecraftEdu, LearnToMod will not be compatible with the new Education Edition of Minecraft until Microsoft implements Minecraft modding into this edition. We hope that Microsoft will implement this in the coming months, but there are currently no definite plans in place. As far as we know, Minecraft Education Edition does not offer an optional vanilla launcher.
If you have any questions about MinecraftEDU vs. Minecraft Education Edition, now is the time to research and ask! The Minecraft Teachers Google group here is very active and a lot of questions which you might have have been answered there.