depending on where the pain is I'd recommend ibuprofren for joint pain and proper warmup and rest for the muscle pain. A mistake a lot of people make when they're just getting into a workout routine is they go at it like gangbusters at first and cause themselves a lot of unnecessary pain which usually forces them out of the routine. Start slow, warm up properly, strech properly, then set a goal of say 10 minutes. Ya I know it doesn't sound like much but the first 21 days is when you build the 'habit' of working out where you 'miss' it when you don't. I'm assuming you and your wife are in it for the long haul so day 1 do 10 minutes, day 2 do 12, and so on until you are at your goal.
Also for FAST fat loss if you can find the time do split cardio and eat the 5 to 7 meals per day. This keeps your metabolism at a high rate throughout the day and will really start dropping those pounds.
A very good suppliment for reducing muscle pain is creatine. It's not illegal and as far as I know does a good job of speeding up muscle repair and helping with the soreness.
When I was working out regularly (which I hope to be doing again soon considering I've got a freaking gym in my house) I used products from
http://www.maxmuscle.com/. There's a wealth of advice and suppliments there that I swear by.
Lastly for lower body pain / injuries I recommend putting a phone book under the foot of your bed instead of trying to sleep with your foot on a pillow. You only need to elevate the injured area slightly above the heart to keep the swelling down and people roll off of pillows when they sleep.
If you feel you have to use heat go for a hot pack that she can warm to her tolerance. I use the hottest stuff I can find but I can understand having a fair skinned wife. Mine recently jacked her knee up and the heat pad really worked better for her.
Good luck
