Can I dynamically change the input clock frequency of the AT91SAM3X8E?
I don't know anything about the AT91SAM3X8E specifically, but I'll guess an answer based on my knowledge of ICs.

Theoretically, there's no reason why you wouldn't be able to dynamically change the master clock frequency in a digital circuit. What you have to be careful of is that during the switching you cannot have any two successive rising edges that violate the maximum frequency of the device. If you imagine switching from one waveform to another when the 'switched from' clock is falling and the 'switched to' clock is rising, then you could get a clock period for one cycle which could be much less than the period of either clock. This would blow the timing on several of the paths and leave your micro in an illegal state.

If you have some way to guarantee that you can properly synchronize the transition between the clocks without creating such a pulse, I can't think of any problem with it.