I ended up overriding GetXpathNavigator in my custom CoreResultsWebpart. This event fires in a late stage, causing the query change not to be overwritten. First I tried to override AddSortOrder in my View, the changes to the query was then lost. Changing sorting worked in AddSortOrder though.
The code I added to GetXPathNavigator was:
QueryManager.UserQuery = query.ToString();
As mamoo noted overriding SetPropertiesOnQdra() will probably work as well. Allthough I have not tested, but will do at work on Monday.
Som offical guidance/best practices on SharePoint Search from Microsoft would really be appreciated.