If the scratching bothers you that much or he/she is scratching you then try using a nail file its safer than using clippers.
Yeah, he will be fine as long as you avoid the pink section of the nail. It might be an idea to get small animal trimmers from your vet - like for a rabbit, because they are smaller, and will prevent major miss-haps. Just remove the sharp section to avoid getting yourself sliced :) Just don't use human nail clippers, as they can split the nail.
You don't need to cut the nails of your kitten because nature is the best teacher for animals. He would soon learn the things you're desiring for.