Embedding fonts is a standard technique, you can find plenty of information around. But note that the <span> may break both searching and hyphenation, depending on the engine.
You could abuse fonts in a similar way, but map, for instance, "é" to your "e + apostrophe", assuming you don't have other "é"s in your Latin words, and then use <span class="whatever">sapiéntor</span> (or simply use accents to mark the stress, as is already done in a number of languages). Then you'd need the reader to support diacritic-insensitive searches, maybe some do already.
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