Crates are great tools for housetraining. I don't think that crating a dog is a bad thing. I think sometimes it is necassary to crate a dog for longer periods of time and I think that it is okay. I leave my dogs in the crate if I go somewhere and sometimes it is for long periods of time. I don't feel I'm a bad mom for doing so.
You may want to rethink crating the one dog and leaving the other out. I think it is very possiable that the one crated will bark at the one out. I hope everything works out for you. Good luck!