Yes, removing the pins will allow the transmission to easily back-drive. But that isn't necessarily a bad thing.
A common practice is to counter-balance your arm, then use a pot or encoder as a feedback signal. Software can then understand the arm/joint location and use the motor to keep the structure located in space.
There are many examples of this on chief....a tag search for "arm" should give many examples of how teams have previously built arm-like systems.
This RUSH Bot from 2005.....you can see the gas springs on the lower joint that help counter-balance the weight of the arm system.
http://www.chiefdelphi.com/media/photos/20302
Chiefdelphi from 2000 using gas springs as counter-balance and dampers.
http://www.chiefdelphi.com/media/photos/12954