Congratulations!  Your canoe now has character.  Nothing has happened to it in a way that cannot be reversed so that it will not degrade it's usefulness or lifespan.

I'd ask the owner to have the kneeling thwart properly installed and to do the best he can to hide the old holes for you.  I guess I'm with those who say you should have refused to pick up and pay for a canoe that was improperly modified but that ship has already sailed.  Now you just have to make the best of it.  

If that's not enough to satisfy you, I guess other steps you could consider taking are:

Search other dealers nationcontinent-wide for a yet-unmodified Bell and if you can find one, see if your dealer will offer a refund and take yours back.  You'd have to pay to get the canoe shipped to you (and maybe the dealer would consider facilitating that step at your expense).  IMHO, this would be taking it a bit too far, but if you are truly that upset, the dealer might consider it.  If he does, you should be singing his praises far and wide to everyone you know as a dealer who stands behind his customers above and beyond the call of duty.

See if the owner is willing to offer some sort of compensatory product or service at no additional charge, such as a new paddle or an additional complimentary modification to the canoe.  Again, if he does, I'd be very vocal about encouraging others to use this dealer.

Overall, it sounds to me like your dealer is willing to meet you somewhere in the middle and for that you should be very pleased.