Importing from Word may carry over extra formatting, which sounds like it may be the culprit. I realize it’s not “automatic” but if you clear the over-rides for a paragraph style, will that correct the reversed English? You may have to go through and apply a Character Style to all the Hebrew text (RTL direction and possibly font) and clear overrides. (Only available with the Middle East version of InDesign.)
I’ve imported Word text, then go through and *find* all Italic text, and apply a Character Style of Italics, bold text to CStyle Bold, Bold Italic, etc. etc. Then I go through and apply the appropriate Paragraph style for each paragraph. Then… where Headings are Bold (in the Paragraph Style) I search for that and remove the Bold Character Style that was applied earlier. (Not really a big deal unless you export to epub – saves extra codeing there.) Then you can clear any over-rides left over and have clean text. Hopefully that makes sense!