I am a lawyer but probably not in your country, so my comments are by necessity rather general and should not be taken as a legal opinion you can rely upon. Speak to a local lawyer if the matter is important enough for you.

When we only look into the narrow issue of renaming files, I do not think this is illegal except when the contract under which you have bought or downloaded the subtitles forbids you from doing so.

Renaming the files and then selling (or even giving them away for free, even when you keep no copy for yourself) may be more of a problem as it may touch issues of copyright.

Writing a program that renames the files will be no more illegal than the act of renaming the files itself and if you want to protect yourself against any claim, you can add something like this to your documentation:

Before using this program you must make certain that renaming subtitle files is not illegal in your country. The author of this program makes no warranty whatsoever in that respect. User's discretion is advised.