You need to set the interrupt input in the micro controller to edge triggered. This way you will only get one interrupt per time the signal from the RTC chip makes a transition. In the level mode that you have now the interrupt keeps triggering as long as the signal from the RTC stays low.

Note that in general you only use level triggered interrupt when there is some way for the software to tell the interrupting source to remove the signal level that caused interrupt.

In your case with the RTC chip the periodic interrupt output has no provision for this software action. It just wants to go as a free running pluse generator.

Hope This Helps.
Mike Karas