I don't see any need in keeping the Mk1 ships. In fact, as I probably suggested some time before already, it'd be good to have all Mk1 ships receive the stats of their Mk2 versions or be balanced around the equal Mk2 ships.
Except for the few ships which don't have Mk2 versions of them, almost no Mk1 ships are used at all, making having two versions of one ship pointless. Money for getting a decent ship can be earned rather quickly, maybe have the people start with a freighter when /restart'ing to make it a little bit easier for new players.
Having "underpowered Mk1 versions" is just a waste imo.