I found a tutorial of adding a real-time google translation button for pdf-xchange editor.
Although pdf-xchange editor is not open source software, but I think it is a good hint for other pdf viewers.
You can download PDF-XChange Editor free version here
You can find the current ASCII-based Arabic transliteration methods here:
None of them does what you are asking for. Are you sure there are enough alphabetic letters for mapping all Arabic symbols? If you are, it seems you need to come up with your own transliteration scheme. If you come up ...