DS1307 RTC not working with CC3000 WiFi shield (I2C bus hangs)
It could be that the CC3000 interrupts are affecting the Wire library's behaviour since the latter is interrupt-driven itself. 
Try disabling the CC3000 IRQ before calling rtc.isrunning() or any other RTC functions. First #include "ccspi.h" in your sketch. Then place WlanInterruptDisable() before any RTClib function call, and then WlanInterruptEnable() after the RTC function returns.

Even if this works, it may affect the functionality of the CC3000, since it increases the chances of missed interrupts. You can search for DS1307 libraries that employ SoftwareI2C instead such as this one. They should be better able to recover from the CC3000 interrupts.