KF8 format supports Hebrew rtl properly. You should not need to 'fix' anything. The HTML source needs to be properly marked up.
Also, you should be able to send such ebook files to Personal Documents service now, as it preserves KF8 formatting (something that was added recently). However I don't know if it will properly convert .doc/.rtf/.txt files in Hebrew (probably not). Send To Kindle browser extension doesn't, it seems. So you may need to learn how to create kf8 files (or use Kindle Previewer or kindlegen to convert epub files you may have).
And the pd conversion service will only create mobi7 which does not supprt rtl.
Consider creating kindle-sized PDF. It is WYSIWYG, easier to author.