Most likely it will not effect the image noticable, but there's one way to find out.
As far as the company, don't you have the option to return it (not exchange)? Personally, I'd do that, even if it was going to cost me a few dollars, and I would buy the same kit from a reputable company like B&H or Adorama. It's be worth the money to me to not support a company with lousy customer service.
Barring that, if the defect is in the glass it should be a no-brainer that it's not your fault. But with a lousy company you never know. If you can't return it for whatever reason then I guess you have to decide if it's worth your time and energy to deal with it, or just try to forget about it. If you can.
There are only two solutions. Live with it or return it. I don't think your new camera lens should have a defect but you ask if it will impact image quality and I'm thinking, "Will I ever forget about that defect?" which to me would be almost as annoying as having to be worried about image quality. It's a psycological thing.
If you do return it, don't be surprised by being asked to pay return shipping. If you return it for replacement and the seller is amenable to replacing it, I would imagine you'll not be charged for shipping a second time.
I actually spoke to Canon also but I do not know if the guy really knew what he was talking about. He said that a speck on the lens would show up as a speck on the photo...
He doesn't know what he's talking about. Grab a small piece of paper, put it on the lens and take a picture. You might be surprised at how little it impacts the final image.
You know the choice you have to make, the rest is up to you. I know exactly what I would do: I'd send it back, tripod and all, and buy from someone else. And I'm not obsessive about specs on my lens. If something was going to bother me then it's a no brainer.
Are you saying that it costs $200 to ship the kit? That's not right, it shouldn't cost near that much. Amazon would be broke if it cost that much. I would find a slower, cheaper method to send it back. Or I'd fight like hell that they sent me a defective product and they need to pay to ship it back for an exchange. Squeeky wheel gets the grease. Raise hell.
A pin piont scratch will NOT show up in any of your photos. Period, now you know. But how much larger than a pin point will show up? To convice yourself, take a few snaps of your white ceiling. Or go outside and snap a blue sky. Stop your lens down some but try several f-stops. You must remember the stuff on the lens is OOF. So the sensor will never see it.
Some smudges can reduce contrast and a keen eyed person can see it.
Now the question, should you return it. And the correct answer is absolutely. Now you have that part answered, also.
Send the entire kit back and buy one from B&H or Adorama. Do it today!
The store the OP purchased from appears to be a legitimate Canon Authorized retailer, in business since 1985 and has a good return policy. I see no need to punish them for a problem that fairly belongs to the factory.