I agree wholeheartedly. Users shouldn't have to edit commercial books just to make them readable.
The fault actually lies with Macmillan. They're the ones who publish Peter F. Hamilton, and they also published the books I found to be faulty. Write to them to complain and tell them to fire the idiot they have who can't follow basic principles.
To make the edits, first unencrypt your book as detailed in the thread linked above. There are a couple of ways to fix the book, both are free. Be sure to work on a copy of the book just in case.
The simplest is to install
Sigil. Just open the epub in Sigil and save it, don't do anything else. Sigil strips out a lot of code that isn't strictly necessary, and will also strip out the faulty encoding parameter. This should work fine with faulty English-language books from Macmillan, but sometimes Sigil can mess up the ToC.
The alternative, which involves less radical change to the original code, is to open the book in an application like
epubtweak, which is free and a convenient way of looking inside the epub. Go through the list of files, selecting each .html file and clicking 'Edit File', which will make it come up in Notepad. Then just take a look at the first line of the file and change
encoding="ISO-8859-1"
to
encoding="utf-8"
then save the file and move on to the next.