I travel often on SE and can't say I'm surprised. We've known for a long, long time that High Speed services would change during the Olympics and Paralympics. To be fair, they haven't changed all to much. For me personally, the frequency has gone down from 2tph to 1tph (to Faversham), which isn't a drastic change and also, trains will still run until about 2:30am.
I appreciate that High Speed services will not run to Margate or Dover (I think), but they will still run to Ashford where you can change to services to Margate and Dover. An inconvenience though.
As far as mainline services go, they're not too different. Okay, main stations will be crowded and certain locations will be entry and other locations will be exit inside the station as well as services being very crowded.
In all, they're not a huge surprise, it's to be expected and we've had a lot of warning.