Replace the bearings- if you want 100k then it's a small price to pay.
A scratch? Did it break a ring, or lose a valve? Why do you think that it's too deep for a hone? Have YOU miked the bore on all?
I think it will be fine as a stock rebuild- I would check the spec.'s on ring end tolerances, and see if you have enough room to expand out to the groove depth and maintain the ring groove integreity without it wallowing out the land.
If so then- hone away (make sure that you do them all)
If not then you would have to bore.

That's the way I see it. But I'm a body & paint guy.