This is an issue that seems to come up perennially.
The Solr docs caution that index-time synonym expansion should be preferred to query-time synonym expansion, due to the way multi-word synonyms are treated and how IDF values can be boosted artificially. But query-time expansion should have huge benefits, given that changes to the synonyms don't require re-indexing, the index size stays the same, and the IDF values for the documents don't get permanently altered.
The proposed solution is to move the synonym expansion logic from the analysis chain (either query- or index-type) and into a new QueryParser. See the attached patch for an implementation.
The core Lucene functionality is untouched. Instead, the EDismaxQParser is extended, and synonym expansion is done on-the-fly. Queries are parsed into a lattice (i.e. all possible synonym combinations), while individual components of the query are still handled by the EDismaxQParser itself.
It's not an ideal solution by any stretch. But it's nice and self-contained, so it invites experimentation and improvement. And I think it fits in well with the merry band of misfit query parsers, like func and frange.