Unfortunately there's no way to prevent Webkit from using font information available to the host system, or restrict it to a subset. But at least this way anyone who runs into the problem will know that the place to fix it is in the css, rather than trying to alter a preference in Sigil that will have no effect on the ereader whatsoever.
An increasing number of ereaders are coming out with a variety of fonts available as stock (the iPad [though you need to add Apple's magic file to enable them properly], Kobo Touch and Sony T1) and if their UAs are correctly coded those fonts should be exposed and usable from the css without having to embed them.
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