I'm not sure you'll get a much different answer here than you did in your previous question...
But anyhow, assuming your module properly sanitizes the input of the script paths field, it's still potentially dangerous to the extent that:
- your users could be untrustworthy, and
- your users could add arbitrary scripts to the file system
- your users may not be able to write safe scripts
So for the most part, this boils down to an issue of trust, so long as the architecture is as described.
To deal with the first item first, it's possible to deny roles upload privileges, so you can prevent them uploading anything or everything if you prefer.
For the second point, the key word is "arbitrary". Drupal has a hook, hook_library that allows you to define js libraries that can be added and referred to from code. You could use this hook to define a preset collection of libraries that your users could add to individual pages (if, as I mentioned, you only need to offer a choice of libraries, and not unique libraries per page).
But I'd suggest rethinking the architecture. For example, if users need to add a unique script to each node, I'd wonder if it would be possible to abstract out what is common to each script, load that script on every relevant page automatically, and let the users pass configuration options through the form fields instead (or e.g. even upload a json or other structured data file which could be sanitized/sanity-checked in PHP before being output to the page).
Alternatively, if you just need to offer your users the option of one among several libraries, and you already use the Context module, you could use a module like e.g. RE Context Libraries to add js files to individual nodes (disclaimer: I wrote the module).
This would allow you to restrict the insertion of libraries to those you've pre-approved, as well as allowing you to piggy-back on the Context module's permissions (though I'd note that the Context module's permissions may not be fine-grained enough if you have many users).