But, I do peek into save files on occasion using this tool just to check what scripts are active, etc. never uninstall a mod (especially that has scripts) in an active game then you won't ever need such a utility. To be honest, if you use sound modding practices, ie. I've only had to use its 'script instance removal' tool once when I removed a scripted mod and that wasn't in my current game. However, I wouldn't use this quite yet without keeping a backup and being willing to revert if necessary, but I'll be keeping a close eye on this tool - I think it's really promising, and even if it turns out to be flawed, its nonetheless a valuable contribution to the community that can probably be fixed or improved if needed. I tried this on several saves with orphaned scripts and it appeared to clean them all out flawlessly. Another handy feature is that it allows you to change the value of variables in different script instances, which can be used to fix erroneous scripts, infinite loops, or even just to customize variables of a mod to something that you'd like better.

This tool appears to be much more capable of targeting specific scripts, versus previous tools that only tried to remove the entire script data block from the save. By default, when you click 'FixScript Instances' it appears to remove all scripts that are not attached to a reference, which are the scripts that usually are causing problems and only arise from uninstalled mods or orphaned magic effects. But preliminary tests seem pretty promising to me - it can remove orphaned scripts extremely well, even the kind that previously could never have been repaired, infinite loops, etcetera. As Crimson13 says, it's something to be wary about.

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