Vernier, the company that produces Logger Pro, is quite generous in terms of its licensing. Schools can pay an affordable site license fee, and that includes the license for not only school computers but even for students to put it on their home computers (Logger Pro 3 site license allows your students to install Logger Pro 3 on their home computers).
It's fairly easy to package Logger Pro for Munki. The Mac version of Logger Pro is distributed as a password-protected .dmg (disk image). You just open it up, enter the password Vernier gives you, and then inside you'll find a .pkg installer file. Just drag that over to your Munki repo and run a munkiimport on it. That's it.
23 November 2015 Update: Actually, I found it there's one extra step you have to take. Install it on one Munki client, and then run this command:
If you don't do that and you do later download a newer version of Logger Pro, Munki won't know to upgrade the old version, because it won't see a difference between the two.