Is there any way to make a ship unusable by the player?

[SkyRender]

I'm trying out the mission builder, and I can't find any way to prevent the player from switching a ship I've put into orbit around Eeloo.  I'd rather have them start at the Space Center and send a rescue vessel to help out said Eeloo-orbiting ship, but I can't figure out how to do that.  Any help?

[GKSP]

I haven't built a mission yet but have started playing them.  You could try putting some required waypoints down in a launch ascent path from the Space Center.  Sure, people could just launch a ship then switch, but it would encourage the use of a ship launched from Kerbin.

Alternative: If the mission requires docking, you could remove the electricity from the ship and force the player to send a small bit of EC on a Kerbin-sent ship to open panels or something of that matter.  It would render the ship useless until encountered by a manually launched vessel.

[oAsAo]

I think you can explode ship and fail mission if player switches to it)

[KerikBalm]

Have it have no control... no probe core and no kerbals? then there's nothing that can be done until a kerbal boards.

Alternately, it can have a probe core, and an antenna, but no EC to power the probe core. You could have some deployable solar panels that a kerbal has to go to and manually deploy... or dock/claw a probe ship to it and provide the power needed to operate the ship...

Then they can switch to it, but can't do anything with it except look at it