If you've seen the behind the scenes documentary furious gods the Deacon Puppet did kinda of come across as stoic in terms of natural fluid movement.
http://vignette1.wikia.nocookie.net/prometheus/images/8/8c/Deacon_prop.jpg/revision/latest?cb=20130227185716In the final film thy clearly applied cgi.
Is it just of matter of how many takes they took they felt that it didn't quite look convincing, or could it have been just to be on the safe side?
Scott had a tough time filming the Chestburster Scene form the original Alien, set up, timing, technical difficulties ect but though it was clearly a puppet your caught in the moment and believe that the puppet is a real creature, they used the right angles and timing capturing the scene perfectly.
It is just a matter of Lighting the Set, not wanting to resort to footage which differs from the story boards and High Definition Footage makes it harder to convey the old tricks of practical effects to work?
While I myself and not apposed to them applying cgi, I suggest they use it accordingly, or else we'll get what happened to The Thing 2011 prequel, with all the practical effects erased by the cgi.