I've used Sigil many many times to convert to hebrew epub. All I do is copy from word (or oo) and paste into sigil, then right-align, select the headings for the table of contents and some meta info and I'm ready to go.
I've used the same method for hebrew pdfs (copy, paste into word and then paste into sigil), but with less success because of the source pdf themselves that I was using. Are you sure your problem is with the conversion process and not your e-reader?
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