Use the proper charset in you website according with the characters you use, that is the correct solution from my point of view. What your are trying is some work around that don’t fix the real issue.
You must note that UTF-8 is the standard enconding recommend for internet nowdays. ISO-8859-1 was considered the standard for 4.01, although most of the websites went with UTF-8 because of the enconding problems ISO-8859-1 had. In XML and HTML5, UTF-8 is the default character set as it is for WordPress since version 3.5. Even further, WP 4.2 will use, when possible, utf8mb4 in database (four-byte UTF-8 encoding, previously it was using utf8mb3) to handle the full range of Unicode characters.
Also, from a practical point of view, it is easier to change the enconding charset of the website than filtering the comments and I tink you will have advantages and no disadvantages.
PD: You may be facing a XY problem in your question. You ask about your intended solution (filtering comments) when your real problem is another (using the correct enconding).