Do Sophos and Spotlight conflict and if so, how can I run both applications without problems?
They don't conflict. Spotlight is a pig on any first run on a newly accessed filesystem. On the other hand, Sophos will double the load caused by controlling all these filesystem accesses.

I suggest you to let Spotlight terminate its heavy initial run alone
by temporarily turning off the On-Access control of Sophos:


I also suggest you to turn off the scan on Files on network volumes, because this will load your Mac, your network and finally
your network volumes. On a well managed network, this scanning should be
run directly on the storage servers.

Once this 1st run terminated, Spotlight will less tend to be a CPU and I/O hog.