Whether ads are shown on a video is up to the content owner of that video. It's not something that the embedder can control.

If you had permission from the content owners of the videos to upload copies in your own account, and then ensured that your account was set up with monetization turned off, then that would prevent ads from showing during playback. It's up to you to work out that arrangement/permission with the original videos' owners, of course.

(It's also worth pointing out that if your goal is to help non-profits raise money, then allowing them to monetize their video playbacks is in line with that goal...)