I think etched would look much better. I doubt I'd get them if they were cut through.Are you planning on etching the logo into the sill or actually cutting the logo out? I'd personally prefer the logo to be cut out so I could put the EL panels in if I decided to. That way the guys who didn't want EL won't have to worry about the cost or hooking them up.
AND, what will be the overall size of the logo? I'll email these people again and see how much a panel would cost.