As far as I'm aware of, if you are using a default installation, which just stores its images in its local images/ folder, then all MediaWiki does is to create the thumbnails and that is all. There is no database entry or anything about them. The image page in the image namespace checks for existance of the according thumbs and if they are present, they are displayed in the "Other resolutions" link. If a size, which does not yet exist, gets requested, MediaWiki will create that size.
So: In this situation, removing thumbnails should be safe.