If you are preparing your returns together with a spouse, then both returns are in the same file, so both will be using the same version of TurboTax. So, even if only one of you is self-employed, you'll both be using the self-employed version, and will both be charged the same. 

If you don't want to use the same version as your spouse, you can prepare your returns separately. But in your case, you need Premier to be able to enter a T3 slip, so both you and your wife would still pay the same.