Using MyIsam is probably your best and only bet to be able to use a spatial index. You might consider storing the data in an innodb table and then export data continuously or by batch, according to your needs, to a myisam table. Then use the myisam table for your queries.

I wouldn't trust myisam as storage engone if data is of importance.

Seems like you figured out the solution yourself.

Using MyISAM is probably your best and only bet to be able to use a spatial index. You might consider storing the data in an InnoDB table and then export data continuously or by batch, according to your needs, to a myisam table. Then use the myisam table for your queries.

I wouldn't trust myisam as storage engine if data is of importance.

Seems like you figured out the solution yourself.