Adding anti-aliasing filter to op-amp before ADC, clock frequency or sampling frequency?
The MCP3202 has an on-chip sample and hold. Don't make assumptions about internal RCs that work at the Fclk frequency.
You can ignore Fclk, as this is an 'implementation detail' of the ADC. It's important if you're programming Fclk, it's irrelevant if you simply want to use the ADC at whatever rate Fclk sets it to.
The ADC has a maximum sample rate of 100 kS/s, but you can choose a lower rate if you don't want to handle that throughput.
You want to process signals up to 3 kHz. By Nyquist, that means you need an absolute minimum rate of 6 kS/s, at which you would need an unfeasibly good AA filter. To work with a practical AA filter, you need a somewhat higher sampling rate.
You need to know how you are going to be processing the results of your ADC measurements before you design the AA filter.
Are you going to do frequency selective analysis digitally? In this case you only need the AA filter to protect your samples from aliasing. For instance with a 10 kS/s sample rate, the AA filter would have to pass 0-3 kHz, and stop 7 kHz and above. This allows a very generous transition band, making it easier to design. For instance, any noise at 6 kHz that gets aliased to 4 kHz will be ignored by your subsequent analysis stopping at 3 kHz.
Alternatively, do you want every sample taken by your ADC to be valid as it is without further analysis? In this case with 10 kS/s sampling, your AA filter should pass 0-3 kHz, and stop at least 5 kHz (Nyquist) and above. However it will be beneficial to stop from as close as possible to 3 kHz as it can to remove as much noise above 3 kHz as possible. This then gives you a filter flatness/size/performance tradeoff.
You'll notice that in neither case do we use the Nyquist rate directly to specify the AA filter, but via the input bandwidth, and the sort of analysis we want to do subsequently.