Thanks for the replies Rizla. Scripts are left-justified except for dialogue, which is left-justified within a narrower column in the centre of the page. The problem is less about not being able to convert them (which would only be an issue with a relatively small number of especially poor-quality scans) than not wanting to lose the original formatting (most notably pagination). That's also why PDF is the most suitable format, since .html documents don't have pages at all.
Edit:
Here's a random example that's roughly representative of most of the scripts I'm talking about.