you will have another problem whan you change to sharepoint mode, as you will need to create a brand new SSRS db as you cannot run a native mode database in a sharepoint mode ssrs configuration or the other way round.
getting the report history shouldn't be much trouble as long as the catalog hasnt changed in terms of where objects are stored, if the paths on 2005 match the paths on 2008 its a simple join to catalog and history and snapshotdata replacing the 2005 report ids, for that stored in 2008, you will need to do this again when you switch modes, so I would suggest switching modes now then doing the history import.