Hi, unfortunately your question\issue is not clear and your post doesn't indicate if your script is OOB or custom?

As the community does not have visibility of your instance configuration, it is not possible for anyone to assess the impact of any changes you intend to make. As a rule of thumb DOM manipulation is not best practice for customizations.
If the code\script is OOB then you should not delete it and unless you are sure that it will not impact your instance then you should not set it inactive.
For custom code that is no longer used I would not delete but instead set inactive.