Have you tried this type of grate:
Amazon.com : UGODOG Indoor Dog Potty : Pet Floor...
My Teddy has severe separation anxiety so I totally sympathize with you. If your dog is going in the crate, the crate may actually be making the situation worse since confining dogs with separation anxiety can actually freak them out. Teddy has, thankfully, grown out of going in his crate when he's freaked out but I do not believe I could leave him out in the open whilst I was gone and not find 'presents'. You can talk to a behaviorist about this because there are some treatments, like desensitization, which could help since you may be unwittingly doing something that is making this dog feel insecure. If that doesn't work, it could be the anxiety is innate and you will just have to try your best to keep your house clean and your little guy safe while you're away.
In the mean time, try a pen with a top on it and use this grate. Ensure you are leaving treats even if he doesn't want them. Treat balls keep Teddy occupied. Those are little plastic balls which dispense treats as they roll around. True, he goes all sweaty and crazy trying to get the treats out but that's better than jumping up and down in the same spot (which happens to be on poop!) for hours!
I have to return to work full time soon, myself, so this is a worry for me, too. It's 2 a.m. here so I feel I am kind of rambling so if I think of anything else that I can suggest, following some much needed sleep, I'll come back to you!