With today's technology, I wouldn't be too concerned with CF. Chances are, Giant reps aren't concerned in the least about your situation if the symptoms aren't there. Yes, you may see some hairline cracks, but without further evidence of an expansion of said possible cracks and/or loss in stiffness in the frame, cracking noises from hard OOS, etc. it's possible they come across situations like yours all the time, and the conclusion is all the same. Aesthetics, not a functional concern.
Is there evidence out there of how many percentage of frames are repaired by reputable brands over the years? Perhaps. And that'd be a revelatory data mine as far as I'm concerned... but currently it's not an issue to me.
I have a small crack around the BB area of my CF steed, which I noticed ~1200 miles ago. Since then, I've put about as much force as I'll ever put on it (being 265lbs and doing a reasonable amount of sprints and OOS climbing), and haven't noticed any loss in stiffness while sprinting, or heard any noises to be concerned about. The whole notion of CF bikes "assploding" while riding is such a cliche to me so as to be laughable, especially if riding a bike from a known brand that has been producing frames for the last couple decades.
If any concern, I'd take the bike to another LBS for a second-third-fourth opinion. Worst case, get it repaired. $300 for a frame to get repaired so that it's stronger than before sounds a lot more cost effective than plopping down 4 figures for a new setup, if all things are the same.