Spatial Index on an InnoDB table
Yes, that's the best I think. You have the benefit of both InnoDB (referential integrity) and MyISAM (spatial indexes.)

The only technical difficulty is to ensure that the MyISAM table is synchronized with the InnoDB one. This can be done either with triggers or by stored procedures (so every operation on the InnoDB table is done through a procedure.)

Another "benefit" is that since the coordinate values are duplicated at both tables, you can skip backing up the MyISAM table (or backing up separately) and have a procedure to recreate it after a database restore. You probably need a procedure to check periodically that that the two tables are in sync, too.

To speed up queries that need the spatial index - and if the table is not huge - you can make sure that the index is loaded in memory in advance, even in a separate cache. See LOAD INDEX INTO CACHE syntax and Multiple Key Caches