From what I've read battery issues with the 4S can occur when you setup the phone from an iTunes backup, ie restore all your contacts, photos, settinggs etc from a previous iTunes backup.
There's even a ZDnet article where an iTunes backup from a 4S with battery issues (we'll call it phone 1) is put onto a 4S that previously had no battery issues (we'll call it phone 2) and it causes the phone 2 to have the battery issue. Read it for yourself below;
http://www.zdnet.com/blog/hardware/test-suggests-iphone-battery-issue-not-a-hard ware-problem/16250
Instead of restoring from an iTunes backup, try backing up all your content to iCloud, reset you phone to factory default, then restore your files etc from iCloud.
Be aware though that iCloud will only backup 1000 photos, so if you have more you'll lose some!
EDIT: alternatively, before attemtping a full restore via iCloud, try simply resetting all settings. According to the below article it can fix the battery issue. It makes sense that it would help if the problem is caused by a setting that restored according to a previous backup. I've just tried it on mine, fingers crossed yo!
http://www.gottabemobile.com/2011/12/02/how-to-fix-bad-iphone-4s-battery-life-in -5-minutes/