They'll freak out, just be quick. A good way is with a large bowl, just scoop it up and put it in the bucket (filled with tank water). I use a net, but never keep the axolotl out of the water for more than a second or two.
What size pebbles? These can be just as dangerous as gravel. I've had axolotls bite (and thankfully spit out) pebbles up to 2 cm across.