I've run into an issue with opening a new window in safari (both ipad and desktop versions) that revolves around the popup blocker. Basically I've found that if window.open isn't called from a click event, safari will block the popup.
The event that is calling window.open is currently onchanged from a list box.
Is there any way other than switching which event we handle to trick safari into allowing a popup in this scenario? (the onchanged event)
I don't think there is a way to open a new window in mobile safari other than from a button click. Refer to this StackOverflow Question which is similar. I'm not sure if it will work, but you can look at triggering a button click programatically using jquery's trigger() function.
You might also want to look at options of showing a dialog within your own page, maybe using tools like jquery ui.
HTH!