That's perfectly fine. I breed using my Ditto all the time; heck, I'd swear mine literally lives at the daycare. (Pulled it out for a while while trying to finish SoulSilver, and also because I make the Egg move offers for breeding.)
I've discovered that Golduck can learn all three of the STAB Water moves that can be bred into Totodile. That means Aqua Jet, Hydro Pump (powerful stuff there), and Water Pulse. I will see if I can get all three and then you can choose what to keep from there. I know I caught a high-level Golduck surfing around eastern Unova somewhere, so shouldn't be a problem using a Heart Scale or two (besides, I can clone to infinity). :) I can clone my Golduck, use Heart Scales to get the moves on the clone, stick it in the daycare with Croconaw, and problem solved. :D