There's times when messing with core files will cause later problems when upgrading, but I don't think this is one of them. The edits needed to turn off nofollow do not affect how weblog data is stored or manipulated, so that the worst that can happen upon upgrading or re-installing would be re-enabling nofollow.
In the absence of a plugin or admin checkbox, this is pretty much the only way those of us who don't choose to use it can disable it. For my part, when I edit core files, I comment out the lines I'm changing (rather than deleting them), along with a note saying what I changed, why and when, with my initials, so I can find my changes weeks or months later. If between now and the next upgrade someone writes a plugin to flip nofollow on and off, it will be a simple matter to undo my edits and activate the plugin instead.