They should take them since they are not Disney owned. I just want to add though that the prices at this McDonalds are considerably higher than the average McDonalds as they have a high rent to pay and Disney dictates their prices.
If you want to go to McDonalds, there is a McDonalds straight across the street from Downtown Disney in the Crossroads Shopping Plaza. Just head down Hotel Blvd and go straight through the signal that crosses over 535. You will see the McD's on the left as you cannot miss it.
They will definately take your coupons,gift certificates at this location.