Can't you use WebSQL? ( see question What is the maximum size of a Web SQL DB in iOS (Safari) on the iPad? How about LocalStorage? ).
If you coded it for LocalStorage you could easily use that LocalStorage API to access WebSQL on iOS devices...
Perhaps a jump to PhoneGap would solve some of your problems?
Do you need to store ALL data from your database?
I have a library for doing Syncrhonization, it's LocalStorage at the moment but the next update will allow me to use nearly any storage mechanism as it only needs one index. Purging data that is no longer required is on the list too... It's located at https://github.com/forbesmyester/SyncIt and you can even see a presentation courtesy of SkillsMatter / LondonAJAX.