remypal,
as far as i can see, the worst that will happen is that your pup might get a bit confused between going outside and going on the papers. however, from your thread it sounds that remy is doing just fine so far. by confused, i mean that remy might just take a bit longer to make the final jump into becoming completely housebroken, due to the pee pads. but in your situation i think you are doing the best that you can to ensure that your pup remains stress free. a pup should not be left alone in a crate fo the length of time. it's nice to hear that you've done some research with your vet in regards to that. also nice that you set up the pee pads near the door so that way remy is at least still being made to make an effort to get as close to going outside as possible. all of those things should make that final step even closer. when remy is about 7 months old, she should be able to hold it for that length of time, and since it is only for three days out of the week, it shouldn't be too much of a problem.
is there any way that you can have a relative, family member, or neighbor come by and let remy out for an hour during the three days that you and your husband are gone? that might help in crate training her, and would also allow her some exercise. the break would also allow her to remain in the crate for the duration, since the break would most likely come in between the 8+ hour duration.