It seems that the only way to get rid of the magnifier in iPad Safari is to use: -webkit-touch-callout: none; -webkit-user-select:none; user-select:none; They work fine. But in the scenario created here (http://jsfiddle.net/bakhshi/qbvhx5cx/show) it re-appears and does not go away even if you refresh the page. The only way to remove the magnifier again is to close the tab and reopen it. it seems that when you dynamically create a focused textbox and then remove it *while the keyboard is open* the problem occurs. Note that if you close the keyboard before removing the textbox (before touching the blue div in the provided example) it behaves normally.
<rdar://problem/18072846>
It's interesting! even if you do not remove the textbox and just set it "readonly" it results in the same problem. So just as another way to remove the keybaord, you can set the "readonly" attribute and then remove the "readonly" after a while( settimeout).