You can totally put the mod in just shortly before the ceremony starts and delete it after graduation.
It's like with the mod that gets rid of pimples that have been stuck on a young adult Sim.
If you don't attend graduation, I had it happen that my Sims didn't get the graduation traits and/or diploma. That might be an unrelated issue though. The Sims 4 isn't great for rotational gameplay.
I do have quite some Sims struck with midlife crisis goals and no midlife crisis to complete (also no milestone for getting through Midlife Crisis) because I rotated away from the family with the midlife crisis moodlet still active. I will certainly not do that again because it bothers me a lot.
Back to graduation: I did have issues with the graduation ceremony not loading at all when I set all teens in my save to 'played' before the ceremony. That was before I decided to do a mod for it, though, so it's been a while.
