You can also just exclude the transactions if your reimbursements are equal to your expenses. (Obviously that won't work if you get a set per diem for food regardless of what you spend, though.)
Or could you just use one card as your dedicated work expenses card and add a checking account that you get your reimbursements sent to? My husband has a work credit card that he gets reimbursed for, but occasionally he has to pay it off before he gets reimbursed. It was totally screwing up our finances so he opened a second checking account that he uses just for work reimbursements, and that account isn't connected to our mint.com account.