How do I get spatial index feature if I mainly use innodb?
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.