I enjoy spelling Latin and Greek loan words according to their original spelling, e.g. præcise and œconomy. Might there be a convenient way to add these to the spellfile (manually) and at the same time mark their modern counterparts as bad (i.e. the words that in each case have e for æ and œ)?
Perhaps the very best solution would be a script that looked up all words containing æ or œ, and, if the same word with e were considered correct, would accept the variant and mark the original as bad (and otherwise do nothing).