Why doesn't she open her own checking account if she's working?
You beat me to this, Sandi -- I was going to ask the exact same thing.
Zew, I would suggest that you each maintain a separate checking account, and then continue to have the joint account as well. Agree on a set allocation, based on your incomes, that the two of you will contribute to the joint (family) account. For example, if your total joint HH expenses are $3000/mo, and you earn twice what she does, you'd contribute $2000 into the joint account and she'd contribute $1000.
She can then use her own account for going out with her friends, in any way spending money on her affair, etc.
Your paycheck should be direct-deposited into your new SEPARATE account, with just the pretermined amount (the $2000 above) then automatically transferred over to the joint, family account.