It is now possible to transfer crew members without EVA between docked ships.
The KSP wiki has a section explaining how at the bottom of the Crew page:
... in case of transfer option, we can click on an another cabin with free seat in the same craft or a docked together group ...
Not sure which version this was addedNot sure which version this was added, but the screenshot on the wiki is dated October 2014.
EDIT:
This was added in v0.25 - see the release notes on the wiki that has a section stating:
Crew Transfer
Kerbals in the same vessel don't need a spacesuit anymore to switch seats. Just click the crew hatch and select Transfer to tell them to go sit somewhere else.