Low-pass Filter with zero drift amplifier
Can an auto-zero or chopper amplifier be used in a low-pass filter to
  remove a high frequency carrier?


Yes, if you really are using it as a low pass filter, the fact that its a chopper doesn't interfere with the signal unless but only if the auto zero/chopper has a unity gain bandwidth of greater than 100kHz (or whatever your frequency of interest is that might conflict with the chopping frequency ). The reason I say yes, is because most all chopper/auto zero amplifiers have a unity gain bandwidth in the Mhz range. The chopping frequency is higher than that of the unity gain crossover point. 

The worst case scenario is the chopper/auto zero amplifier is chopping at 100kHz (or a harmonic). Because these amplifiers modulate and then demodulate signals, if the demodulation happens at the same frequency as the input bad things happen. Usually the chopping frequency is stated in the datasheet, or can be seen in the noise diagram of the amplifier. 

I have had issues with this, I had an auto zero amplifier that was picking up RF in the range of 70-700Mhz and it was causing a shift (ever so small) in the amplifiers output. I put an RF low pass filter on the front end and the problem went away, later on analog devices released this part with the EMI filter built in:



So if you are having problems with a chopper op amp, it may be useful to use a passive low pass filter followed by a buffer amplifier at unity gain (or thereabouts). 


  Would I be better off using a passive filter and dealing with any
  residual aliasing of the 100kHz carrier digitally?


There are two options, an active filter and making sure the any high frequencies that are to be filtered are within the bandwidth of the amplifier (and thus well away from the chopping frequency)

A passive filter followed by an impedance buffer (this would be the only way to go if you had a frequency on the input that was at the chopping frequency)