"An algorithm is allowed to show a pop-up if:
 - it is running in the context of an activation behavior or of the dispatching 
   of a click event, and
 - The click events that led to the triggering of the activation behaviors, if 
   any, and the click events of any event dispatching that indirectly led to the 
   algorithm being invoked, if any, are all trusted."

Testcase 
http://mozilla.pettay.fi/moztests/popup.html
All the browsers open a new tab

Since webkit doesn't support <a>.click() the test case is a bit hacky and
uses <input> element to dispatch click.
I could have of course just dispatched click using createEvent/initMouseEvent/dispatch
(I'm not quite happy with the test case, since it relies
on the implemented "activation behavior", not the totally different thing what 
the spec defines.)

But anyway, the point is that implementations usually allow popups *while* 
handling a trusted click event. Inside the event listener one can dispatch/handle
other events, but that doesn't affect to the popup blocking.
Manually dispatching and handling an event is effectively just a (synchronous) 
function call.