I have tested several workarounds to disable the annoying magnifying glass with css, but on my iOS9 meteor cordova build it appears for a moment and fades out after
Yes, it is related to iOS9. Since you are a Cordova user, this plugin will fix the problem for you: https://github.com/EddyVerbruggen/cordova-plugin-ios-longpress-fix
It has to do with the UILongPressGestureRecognizer executing before handling the -webkit-user-select: none in your css.
I hope this helps you out.
The plugin Frederik mentioned is now build into cordova see https://github.com/apache/cordova-ios/pull/174
To enable the fix insert <preference name="SuppressesLongPressGesture" value="true" />
into config.xml