There the same size (diameter), 700c wheels will normally be much narrower than 29er wheel as 700c is used to describe wheels on road bikes, with 23-28mm tires, where as 29ers will have 2.1-2.4 tires (gota love imperial and metric measurements being mixed up for bike terminology)

The biggest difference between a 700c and 29er wheel will be a 700c has a 130mm OLD hub & rim brakes, and has a 135mm / 142.5 OLD rear hub for discs, but expect both of these to change in the next few years, with road bikes getting disc brakes, and MTB's getting wider (bolt through) rears.

Would check the spacing on your frame, as if you currently have a disc specific frame, it probably has either a 132.5 or 135mm spacing.