As has been mentioned, the base fleet should be left open to outside attack as that is half the point of fleetcatching - if the majority of a player's fleet is home whilst three fleets are out (especially returning), then they are in a bind - but they are in that bind due to their own actions and the obvious way to prevent that from happening is to keep a fleet home.
Its part of the game to get your fleet caught at home. It happened to me twice at the end of last round, and its incredibly good/bad (good in that it was enormously exciting, bad that it killed my planet and only just held onto the top 250
).
However, perhaps if your planet is a certain value (compared to the universe average) then your base fleet is unable to engage in combat. This would go a long way for new players to help keep their fleets alive, as they know that the stuff they have in production will survive, whether they are online to prelaunch their fleet or not. (obviously warnings about ships in Base not taking part in combat need to be clearly stated, so that a player doesnt try to defend himself with ships in the Home fleet and then loose roids because he didnt know they didnt fire etc).
Thoughts?