J
We were up against the same problem. There is no good time to do a full system scan. The way we have remidied the problem was to only run the full scan once a month at around 8:00 pm. Then run a daily active scan and enable real time scanning. We have also given the user the ability to pause or snooze their scan for up to 6 hours, ( 3 hours at a time x2) this way they can let it run while they are at lunch. Also, if you add the exclusions recommended by M$ the scans only take about an hour. And the throtling works now too.
Some things to try, because logging in and seeing a scan drag your system to a crawl in the morning is not how you want you end users to start their day. But if they have to, allow them to pause it. The feedback we got was that it is better than nothing and they understand why the scans have to take place.
D