|So the information you provided of two nics and two gateways is not true?|
"if I remove the gateway, my intranet application won't work"
I don't buy what you are saying. Did you even try my suggestion???? Unless your nic A is on a subnet that has a router to another subnet and then to the internet this statement simply isn't true.
Addressing your conditional routing based on domain oriented, does not work that way.
It also makes no sense if you are in a multi router network to have two nics. What you write doesn't add up.