I think this is a matter of personal choice as I don't see any problem keeping the services running. My personal preference would be to stop the services at cutover to identify any potential issues with the services stopped right away rather than running into any surprises 2 weeks later.
One thing should be kept in mind is that if two different products are filtering the same mail stream in series then the results can not be compared as filtering product downstream will not see the original copy of the message due to addition of headers by the filtering product upstream.
Regards,
Adnan