Take a look at my other answers related to this theme:
- Hybrid apps vs Native apps: Hybrid vs native apps
Mobile App vs Web App - Apple no longer accepting web apps?:
To make a story short. Hybrid apps are still more then acceptable in Apple app store, you just need to accept some guidelines like:
- App must have native look and feel
- Do not use 3rd party payment systems
- Do not use server side technology to render page content, use ajax instead
