Hi, googling for USB voltage... the max. by its standard is 5.25V.
From the ATmega328 datasheet its rated max is 5.5V.
So, I think your board/CPU is safe.
From the topics and discussions I have read the majority of concern is about the low/minimum voltage and the total current draw.
And, here is what I know from experience, the Arduino core software EATS batteries. A recent toy of mine is a simple binary clock, a 9v PP3 died in less than 24 hours! The main loop is running at 100% all the time.
I am experimenting with a delay2() function using timer2 and compare-A interrupt (gives less jitter than overflow) and... set_sleep_mode(SLEEP_MODE_EXT_STANDBY). This all works and my clock keeps time correctly. I have not yet measured the power saving as I was about to move on to PRR – Power Reduction Register - to turn off unused parts of the chip (I'll try using macros in avr/power.h). Finally I will increase the system clock prescaler reducing the system clock from 16Mhz to 1Mhz (or as much as I can). This allows the timer2 to remain in sleep longer, this means delay2()'s precision will be under 1ms (but its accuracy will remain the same!!). I also believe the overall power consumption is reduced by slowing the clock. Then, a final step may be to lower the supply voltage to the ATmega to 3.3V (requires the system clock =<8Mhz) I may buy a clone like Seeeduino (switchable supply voltage 3.3V or 5V) or Freeduino SB (powerdown of FT232 USB-Serial chip) to avoid soldering and take advantage of their hardware power saving modifications to complement the software changes I am working on.
I am going to look at the recent posting of DuinOS.
Hope this gives you some ideas.