IIRC, everyone but Doomsday and Maniac will obey your Return to Base orders once you've left the home base navpoint. That might depend on if you're playing KS or the original version.
The key to WC1, SM1 & 2 when you're having severe problems completing a mission is often to *NOT* follow the plotted nav route, and knowing which missions you can safely fail/incomplete and which you have to simply accomplish a specific goal and forget about all the other navpoints. This comes in handy especially in escort missions - instead of autopiloting to where your escorted vessel awaits, you fly to where they're supposed to jump out, clear the navpoint, and clear any hostiles between there and the escort's nav point. That way you won't have to deal with those hostiles with your precious transport or destroyer's life in the balance.