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I fix obvious typos on the assumption that the original author/proofreader would've wanted them fixed. Missing commas are more troublesome--those are a matter of grammar style shifts over time. If you're trying to recreate the original, leave them as-is; if you're republishing, fix them to current standards. (I fix typos even when I'm re-creating the original unless there's a specific reason to keep them, like fanfic zine archives that want to know what kinds of errors were common before spellcheck existed.)
For a historical archive, keep the scans. Run them through auto-OCR so they're at least somewhat searchable, and put those version away. You can do this in whatever format you prefer. I use searchable PDF & add bookmarks by chapter, and tag them as archive copies. Other options would include tifs and a csv load file that includes the OCR text and whatever metadata you cared to collect (begdoc & enddoc by chapter?), but how that would work depends on what program is reading them. Searchable PDF is simple. It's a pain to convert to other formats later--but it's almost certain it will be convertible with effort, and maybe later we'll find better formats for archiving.
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