I would ask them to redo it with gel pads in there. It seems that since they didn't give you a choice they should make up for it. For free.
I changed the bar tape on my Ruby and the gel pads were fine. I repositioned them carefully and retaped without any problem. I even took the pads off the drops so I could get closer to the brake levers and used those pads on another bike. I have even changed the tape and reused the pads again on the second bike! I would definitely get them to redo the bars WITH the gel pads!